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PMC:7253482 / 17528-20451 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
601 16-21 Species denotes HIV-1 Tax:11676
602 31-37 Chemical denotes glycan MESH:D011134
603 26-30 Disease denotes SARS MESH:D045169
608 2364-2367 Gene denotes Env Gene:64006
609 2358-2363 Species denotes HIV-1 Tax:11676
610 2368-2374 Chemical denotes glycan MESH:D011134
611 2347-2351 Disease denotes SARS MESH:D045169
615 2833-2836 Gene denotes Env Gene:64006
616 2827-2832 Species denotes HIV-1 Tax:11676
617 2453-2457 Disease denotes SARS MESH:D045169
656 63-66 Gene denotes Env Gene:64006
657 442-445 Gene denotes Env Gene:64006
658 840-843 Gene denotes Env Gene:64006
659 1507-1510 Gene denotes Env Gene:64006
660 1600-1603 Gene denotes Env Gene:64006
661 57-62 Species denotes HIV-1 Tax:11676
662 333-338 Species denotes HIV-1 Tax:11676
663 343-359 Species denotes SARS coronavirus Tax:694009
664 436-441 Species denotes HIV-1 Tax:11676
665 525-531 Species denotes SARS 2 Tax:2697049
666 636-646 Species denotes chimpanzee Tax:9598
667 647-685 Species denotes simian immunodeficiency virus (SIVcpz) Tax:11723
668 834-839 Species denotes HIV-1 Tax:11676
669 1501-1506 Species denotes HIV-1 Tax:11676
670 1594-1599 Species denotes HIV-1 Tax:11676
671 185-191 Chemical denotes glycan MESH:D011134
672 313-319 Chemical denotes glycan MESH:D011134
673 826-833 Chemical denotes glycans MESH:D011134
674 933-939 Chemical denotes glycan MESH:D011134
675 1180-1186 Chemical denotes glycan MESH:D011134
676 1463-1469 Chemical denotes glycan MESH:D011134
677 1511-1517 Chemical denotes glycan MESH:D011134
678 1576-1582 Chemical denotes glycan MESH:D011134
679 1631-1637 Chemical denotes glycan MESH:D011134
680 1638-1644 Chemical denotes glycan MESH:D011134
681 1677-1689 Chemical denotes oligomannose
682 1717-1724 Chemical denotes glycans MESH:D011134
683 1782-1788 Chemical denotes glycan MESH:D011134
684 1836-1842 Chemical denotes glycan MESH:D011134
685 1945-1951 Chemical denotes glycan MESH:D011134
686 1952-1958 Chemical denotes glycan MESH:D011134
687 2213-2220 Chemical denotes glycans MESH:D011134
688 2256-2262 Chemical denotes glycan MESH:D011134
689 623-627 Disease denotes MERS MESH:D018352
690 725-729 Disease denotes SARS MESH:D045169
691 1458-1462 Disease denotes SARS MESH:D045169
692 1728-1732 Disease denotes SARS MESH:D045169
693 2033-2037 Disease denotes SARS MESH:D045169

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T99 16-19 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T100 57-60 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T101 104-111 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T102 333-336 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T103 436-439 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T104 717-720 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T105 834-837 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T106 1025-1032 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T107 1501-1504 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T108 1594-1597 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T109 2303-2306 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T110 2358-2361 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T111 2446-2449 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T112 2653-2656 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T113 2664-2676 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T114 2747-2750 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T115 2827-2830 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T64 26-30 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T65 343-347 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 525-529 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 654-670 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T68 725-729 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T69 1458-1462 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T70 1728-1732 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T71 2033-2037 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T72 2347-2351 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T73 2453-2457 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T103 70-71 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 636-646 http://purl.obolibrary.org/obo/NCBITaxon_9598 denotes chimpanzee
T105 671-676 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T106 1306-1307 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 1916-1922 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T108 1998-2000 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T109 2384-2385 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 2412-2413 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T111 2490-2491 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 2527-2529 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T113 2691-2692 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 2722-2723 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 2734-2741 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T116 2802-2803 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T117 2816-2817 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T192 54-56 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T193 104-111 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T194 389-397 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T195 415-417 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T196 589-591 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T197 826-833 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T198 1025-1032 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T199 1107-1109 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T200 1717-1724 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T201 2213-2220 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T202 2332-2334 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T203 2443-2445 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T204 2650-2652 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T205 2664-2676 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T206 2734-2741 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T207 2902-2906 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695

LitCovid-sample-MedDRA

Id Subject Object Predicate Lexical cue meddra_id
T6 398-408 http://purl.bioontology.org/ontology/MEDDRA/10022891 denotes microscopy http://purl.bioontology.org/ontology/MEDDRA/10069374

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T49 223-227 http://purl.obolibrary.org/obo/IDO_0000531 denotes host
T50 654-670 http://purl.obolibrary.org/obo/IDO_0000617 denotes immunodeficiency
T51 671-676 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T52 754-761 http://purl.obolibrary.org/obo/BFO_0000019 denotes quality
T53 1078-1083 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T54 2516-2526 http://purl.obolibrary.org/obo/OGMS_0000045 denotes disordered

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T1360 0-11 VBG denotes Visualising
T1361 12-15 DT denotes the
T1362 16-21 NN denotes HIV-1
T1363 22-25 CC denotes and
T1364 26-30 NN denotes SARS
T1365 31-37 NN denotes glycan
T1366 38-45 NNS denotes shields
T1367 46-48 IN denotes by
T1368 49-56 NN denotes cryo-EM
T8430 57-62 NN denotes HIV-1
T3174 63-66 NN denotes Env
T27555 67-69 VBZ denotes is
T55541 70-71 DT denotes a
T20248 72-82 JJ denotes prototypic
T67286 83-88 JJ denotes viral
T69498 89-94 NN denotes class
T3932 95-96 CD denotes I
T49427 97-103 NN denotes fusion
T80657 104-111 NN denotes protein
T46816 112-116 WDT denotes that
T99370 117-125 VBZ denotes exhibits
T82158 126-135 JJ denotes extensive
T40184 136-143 NN denotes surface
T83381 144-157 NN denotes glycosylation
T34922 157-158 -COMMA- denotes ,
T41135 159-168 VBG denotes resulting
T52094 169-171 IN denotes in
T41086 172-174 DT denotes an
T24478 175-184 JJ denotes effective
T12116 185-191 NN denotes glycan
T66049 192-198 NN denotes shield
T24089 199-201 TO denotes to
T80516 202-205 VB denotes aid
T40146 206-213 NN denotes evasion
T31245 214-218 IN denotes from
T10149 219-222 DT denotes the
T79574 223-227 NN denotes host
T93688 228-236 JJ denotes adaptive
T94198 237-243 JJ denotes immune
T10989 244-257 NN denotes response21,31
T32196 259-261 IN denotes In
T81817 262-267 NN denotes order
T91723 268-270 TO denotes to
T52822 271-280 VB denotes visualize
T6796 281-284 DT denotes the
T38040 285-294 NN denotes structure
T51236 295-297 IN denotes of
T17574 298-301 DT denotes the
T94895 302-312 JJ denotes respective
T2313 313-319 NN denotes glycan
T39465 320-329 NN denotes “shields”
T63649 330-332 IN denotes of
T97323 333-338 NN denotes HIV-1
T48816 339-342 CC denotes and
T59243 343-347 NN denotes SARS
T65533 348-359 NN denotes coronavirus
T26306 360-362 PRP denotes we
T89403 363-367 VBD denotes used
T31852 368-383 JJ denotes single-particle
T56676 384-397 NN denotes cryo-electron
T27050 398-408 NN denotes microscopy
T97416 409-410 -LRB- denotes (
T56321 410-417 NN denotes cryo-EM
T61586 417-418 -RRB- denotes )
T32555 420-423 DT denotes The
T47125 424-431 NNS denotes results
T36239 432-435 IN denotes for
T18889 436-441 NN denotes HIV-1
T12931 442-445 NN denotes Env
T63067 446-450 VBD denotes were
T30265 451-461 VBN denotes reproduced
T57197 462-470 RB denotes directly
T8292 471-475 IN denotes from
T31650 476-484 NNP denotes Berndsen
T37715 485-487 NNP denotes et
T19388 488-493 NN denotes al.51
T9777 494-499 IN denotes while
T55752 500-503 DT denotes the
T50993 504-514 RB denotes previously
T21233 515-524 VBN denotes published
T39264 525-529 NN denotes SARS
T63581 530-532 NN denotes 2P
T16458 533-542 NN denotes dataset52
T19972 543-546 VBD denotes was
T72393 547-558 VBN denotes reprocessed
T49131 559-562 IN denotes for
T60843 563-567 DT denotes this
T69625 568-573 NN denotes study
T12832 575-583 IN denotes Although
T24787 584-591 NN denotes cryo-EM
T29672 592-600 NNS denotes datasets
T9596 601-603 IN denotes of
T45576 604-609 RB denotes fully
T37894 610-622 VBN denotes glycosylated
T35124 623-627 NNS denotes MERS
T87593 628-631 NN denotes S41
T79382 632-635 CC denotes and
T63281 636-646 NN denotes chimpanzee
T35247 647-653 JJ denotes simian
T82138 654-670 NN denotes immunodeficiency
T35287 671-676 NN denotes virus
T14224 677-678 -LRB- denotes (
T81517 678-684 NN denotes SIVcpz
T3442 684-685 -RRB- denotes )
T14676 685-687 CD denotes 53
T32530 688-691 VBP denotes are
T45598 692-696 RB denotes also
T95444 697-706 JJ denotes available
T17171 706-707 -COMMA- denotes ,
T88916 708-712 RB denotes only
T2700 713-716 DT denotes the
T19064 717-720 NN denotes HIV
T16401 721-724 CC denotes and
T74879 725-729 NN denotes SARS
T37597 730-734 NNS denotes data
T46398 735-739 VBD denotes were
T10901 740-742 IN denotes of
T19935 743-753 JJ denotes sufficient
T58744 754-761 NN denotes quality
T47642 762-763 -LRB- denotes (
T27616 763-769 CD denotes Fig. 5
T15042 769-770 -RRB- denotes )
T64790 772-774 PRP denotes We
T12200 775-783 RB denotes recently
T55283 784-792 VBD denotes showed51
T5337 793-797 IN denotes that
T85969 798-806 NNS denotes dynamics
T15501 807-809 IN denotes in
T81842 810-817 NN denotes surface
T53947 818-825 VBN denotes exposed
T58293 826-833 NNS denotes glycans
T78469 834-839 NN denotes HIV-1
T11314 840-843 NN denotes Env
T63261 844-849 VBZ denotes leads
T50401 850-852 TO denotes to
T72222 853-855 DT denotes an
T69150 856-865 JJ denotes extensive
T26975 866-873 NN denotes network
T64977 874-876 IN denotes of
T71776 877-889 NNS denotes interactions
T7784 890-894 WDT denotes that
T35226 895-900 VBP denotes drive
T68570 901-913 JJR denotes higher-order
T34602 914-925 NN denotes structuring
T35212 926-928 IN denotes in
T61552 929-932 DT denotes the
T88226 933-939 NN denotes glycan
T2686 940-946 NN denotes shield
T70456 948-952 DT denotes This
T49009 953-962 NN denotes structure
T80667 963-970 VBZ denotes defines
T33829 971-978 JJ denotes diffuse
T1508 979-989 NNS denotes boundaries
T66208 990-997 IN denotes between
T95551 998-1004 VBN denotes buried
T27513 1005-1008 CC denotes and
T63689 1009-1016 VBN denotes exposed
T23712 1017-1024 NN denotes surface
T90175 1025-1032 NN denotes protein
T66804 1033-1040 NN denotes surface
T71072 1040-1041 -COMMA- denotes ,
T80348 1042-1047 WDT denotes which
T9316 1048-1051 MD denotes can
T90504 1052-1057 VB denotes serve
T42110 1058-1060 TO denotes to
T69932 1061-1067 VB denotes define
T67682 1068-1077 JJ denotes potential
T2204 1078-1083 NNS denotes sites
T70578 1084-1086 IN denotes of
T95274 1087-1100 NN denotes vulnerability
T46703 1102-1109 NN denotes Cryo-EM
T30395 1110-1118 VBZ denotes captures
T87072 1119-1122 DT denotes the
T44958 1123-1139 JJ denotes ensemble-average
T7879 1140-1149 NN denotes structure
T75651 1150-1152 IN denotes of
T66273 1153-1165 NNS denotes biomolecules
T73691 1166-1169 CC denotes and
T31109 1170-1179 RB denotes therefore
T12255 1180-1186 NN denotes glycan
T11220 1187-1195 NNS denotes dynamics
T43250 1196-1203 VBZ denotes results
T52169 1204-1206 IN denotes in
T64021 1207-1214 VBN denotes blurred
T49153 1215-1222 NN denotes density
T2441 1223-1225 IN denotes at
T80700 1226-1229 DT denotes the
T16085 1230-1241 NNS denotes resolutions
T86172 1242-1251 JJ denotes necessary
T28589 1252-1255 IN denotes for
T42839 1256-1264 VBG denotes building
T3599 1265-1271 JJ denotes atomic
T43748 1272-1281 NN denotes structure
T10071 1283-1290 RB denotes However
T88433 1290-1291 -COMMA- denotes ,
T97506 1292-1294 PRP denotes we
T94206 1295-1301 VBD denotes showed
T91691 1302-1305 WRB denotes how
T17411 1306-1307 DT denotes a
T2527 1308-1314 JJ denotes simple
T82430 1315-1326 NN denotes combination
T32469 1327-1329 IN denotes of
T40028 1330-1338 JJ denotes low-pass
T93291 1339-1348 NN denotes filtering
T10413 1349-1352 CC denotes and
T2487 1353-1370 NN denotes auto-thresholding
T78379 1370-1371 -COMMA- denotes ,
T27010 1372-1374 RB denotes as
T32044 1375-1379 RB denotes well
T89162 1380-1382 IN denotes as
T8187 1383-1385 NN denotes 3D
T99213 1386-1397 NN denotes variability
T14190 1398-1406 NN denotes analysis
T81037 1406-1407 -COMMA- denotes ,
T87732 1408-1411 MD denotes can
T9264 1412-1418 VB denotes reveal
T36472 1419-1422 DT denotes the
T15866 1423-1433 RB denotes previously
T33845 1434-1440 VBN denotes hidden
T31709 1441-1450 NN denotes structure
T97881 1451-1453 IN denotes of
T77189 1454-1457 DT denotes the
T22984 1458-1462 NNP denotes SARS
T32877 1463-1469 NN denotes glycan
T15037 1470-1476 NN denotes shield
T70541 1477-1480 CC denotes and
T30415 1481-1488 VB denotes compare
T37461 1489-1491 PRP denotes it
T52236 1492-1496 IN denotes with
T25513 1497-1500 DT denotes the
T63380 1501-1506 NN denotes HIV-1
T80636 1507-1510 NN denotes Env
T69159 1511-1517 NN denotes glycan
T3337 1518-1526 NN denotes shield51
T64033 1527-1528 -LRB- denotes (
T94502 1528-1534 CD denotes Fig. 5
T94581 1534-1535 -RRB- denotes )
T60289 1537-1539 PRP denotes We
T75223 1540-1547 VBP denotes observe
T57545 1548-1551 DT denotes the
T48330 1552-1558 RB denotes nearly
T87308 1559-1575 JJ denotes all-encompassing
T1558 1576-1582 NN denotes glycan
T99824 1583-1590 NN denotes density
T59798 1591-1593 IN denotes on
T56235 1594-1599 NN denotes HIV-1
T14383 1600-1603 NN denotes Env
T33263 1604-1607 CC denotes and
T4213 1608-1616 NN denotes evidence
T91161 1617-1620 IN denotes for
T79082 1621-1630 JJ denotes extensive
T66189 1631-1644 NN denotes glycan–glycan
T48593 1645-1657 NNS denotes interactions
T42535 1657-1658 -COMMA- denotes ,
T14663 1659-1669 RB denotes especially
T44869 1670-1672 IN denotes in
T77065 1673-1676 DT denotes the
T90752 1677-1689 NN denotes oligomannose
T24864 1690-1695 NN denotes patch
T20998 1696-1703 NNS denotes regions
T55492 1703-1704 -COMMA- denotes ,
T69929 1705-1712 IN denotes whereas
T90575 1713-1716 DT denotes the
T59031 1717-1724 NNS denotes glycans
T94235 1725-1727 IN denotes on
T22232 1728-1732 NNP denotes SARS
T7541 1733-1734 NNP denotes S
T66013 1735-1741 VBP denotes appear
T27090 1742-1746 RBR denotes more
T7370 1747-1755 VBN denotes isolated
T67487 1756-1759 CC denotes and
T50530 1760-1764 VBP denotes lack
T21892 1765-1768 DT denotes the
T55852 1769-1781 JJ denotes wide-ranging
T70160 1782-1788 NN denotes glycan
T80844 1789-1797 NNS denotes networks
T83936 1798-1802 WDT denotes that
T81018 1803-1806 VBP denotes are
T68036 1807-1810 DT denotes the
T82951 1811-1819 NN denotes hallmark
T16903 1820-1822 IN denotes of
T2902 1823-1825 DT denotes an
T18742 1826-1835 JJ denotes effective
T88640 1836-1842 NN denotes glycan
T57983 1843-1854 NN denotes shield54,55
T96638 1856-1859 DT denotes The
T9355 1860-1862 NN denotes 3D
T47791 1863-1874 NN denotes variability
T79677 1875-1879 NNS denotes maps
T51290 1880-1883 VBP denotes are
T66740 1884-1888 RBR denotes more
T28675 1889-1898 JJ denotes sensitive
T51626 1899-1901 TO denotes to
T96563 1902-1905 JJ denotes low
T5756 1906-1915 NN denotes intensity
T42122 1916-1922 NN denotes signal
T93380 1923-1926 CC denotes and
T52275 1927-1933 VBP denotes reveal
T65761 1934-1944 JJ denotes additional
T40659 1945-1958 NN denotes glycan–glycan
T18648 1959-1971 NNS denotes interactions
T53697 1972-1974 IN denotes in
T13379 1975-1979 DT denotes both
T61777 1980-1984 NNS denotes maps
T1991 1984-1985 -COMMA- denotes ,
T10706 1986-1993 RB denotes however
T21547 1994-1997 DT denotes the
T89902 1998-2000 NN denotes S1
T24397 2001-2017 JJ denotes receptor-binding
T67026 2018-2025 NNS denotes domains
T98351 2026-2028 IN denotes in
T69700 2029-2032 DT denotes the
T97210 2033-2037 NN denotes SARS
T19203 2038-2045 NN denotes dataset
T21495 2046-2050 VBD denotes were
T3893 2051-2056 VBN denotes shown
T33461 2057-2059 TO denotes to
T68704 2060-2065 VB denotes exist
T1970 2066-2068 IN denotes in
T91066 2069-2073 CC denotes both
T75781 2074-2076 RB denotes up
T44006 2077-2080 CC denotes and
T47879 2081-2085 IN denotes down
T22009 2086-2101 NN denotes conformations52
T80149 2101-2102 -COMMA- denotes ,
T10724 2103-2110 VBG denotes leading
T29355 2111-2113 TO denotes to
T48291 2114-2118 JJ denotes poor
T15651 2119-2129 NN denotes resolution
T15044 2130-2133 CC denotes and
T36313 2134-2145 JJ denotes significant
T78120 2146-2160 NN denotes 2D-variability
T97054 2161-2166 WDT denotes which
T80897 2167-2169 VBZ denotes is
T73857 2170-2179 VBN denotes convolved
T52453 2180-2184 IN denotes with
T12417 2185-2188 DT denotes the
T9415 2189-2200 NN denotes variability
T91463 2201-2207 VBG denotes coming
T37758 2208-2212 IN denotes from
T69399 2213-2220 NNS denotes glycans
T37469 2221-2224 CC denotes and
T7534 2225-2231 VBZ denotes limits
T29335 2232-2235 DT denotes the
T16169 2236-2252 NN denotes interpretability
T54909 2253-2255 IN denotes of
T36751 2256-2262 NN denotes glycan
T68517 2263-2272 NN denotes shielding
T73688 2273-2280 NNS denotes effects
T27520 2281-2283 IN denotes in
T1634 2284-2288 DT denotes this
T15004 2289-2295 NN denotes region
T14842 2296-2298 IN denotes of
T18381 2299-2302 DT denotes the
T85741 2303-2306 NN denotes map
T77710 2308-2312 NNP denotes Fig.
T43639 2313-2314 CD denotes 5
T80136 2315-2326 JJ denotes Comparative
T57723 2327-2334 NN denotes cryo-EM
T19047 2335-2343 NN denotes analysis
T52944 2344-2346 IN denotes of
T86979 2347-2351 NNP denotes SARS
T71022 2352-2353 NNP denotes S
T87387 2354-2357 CC denotes and
T92374 2358-2363 NN denotes HIV-1
T58960 2364-2367 NN denotes Env
T67673 2368-2374 NN denotes glycan
T21302 2375-2382 NNS denotes shields
T48820 2384-2385 DT denotes a
T79466 2386-2390 NNP denotes Left
T16113 2391-2396 NN denotes panel
T98169 2396-2397 -COLON- denotes :
T63629 2398-2407 VBN denotes Sharpened
T90429 2408-2424 JJ denotes 3.2-Å-resolution
T6423 2425-2437 JJ denotes C3-symmetric
T13124 2438-2445 NN denotes cryo-EM
T56273 2446-2449 NN denotes map
T86558 2450-2452 IN denotes of
T37174 2453-2457 NNP denotes SARS
T84496 2458-2459 NNP denotes S
T86959 2460-2462 NN denotes 2P
T75209 2463-2475 NN denotes ectodomain52
T37067 2476-2486 VBN denotes visualized
T22530 2487-2489 IN denotes at
T60171 2490-2491 DT denotes a
T27128 2492-2496 JJ denotes high
T94740 2497-2504 NN denotes contour
T58510 2505-2510 NN denotes level
T66412 2511-2515 IN denotes with
T32176 2516-2526 VBN denotes disordered
T5395 2527-2529 NN denotes S1
T34000 2530-2546 JJ denotes receptor-binding
T54890 2547-2550 CC denotes and
T9018 2551-2561 JJ denotes N-terminal
T68442 2562-2569 NNS denotes domains
T72184 2570-2579 VBG denotes extending
T12801 2580-2583 RP denotes out
T26493 2584-2588 IN denotes from
T4854 2589-2592 DT denotes the
T35333 2593-2600 JJ denotes central
T39891 2601-2605 NN denotes core
T4786 2607-2613 JJ denotes Middle
T40721 2614-2619 NN denotes panel
T2753 2619-2620 -COLON- denotes :
T68941 2621-2629 JJ denotes Low-pass
T98545 2630-2638 VBN denotes filtered
T5712 2639-2640 -LRB- denotes (
T65635 2640-2643 NN denotes lpf
T36825 2643-2644 -RRB- denotes )
T66628 2645-2652 NN denotes cryo-EM
T90188 2653-2656 NN denotes map
T57750 2657-2659 IN denotes of
T25808 2660-2663 DT denotes the
T69826 2664-2676 NN denotes glycoprotein
T87240 2677-2687 VBN denotes visualised
T62278 2688-2690 IN denotes at
T88612 2691-2692 DT denotes a
T55069 2693-2696 JJ denotes low
T38898 2697-2704 NN denotes contour
T68027 2705-2710 NN denotes level
T69920 2711-2716 IN denotes along
T22579 2717-2721 IN denotes with
T51416 2722-2723 DT denotes a
T26917 2724-2733 JJ denotes simulated
T72481 2734-2746 JJ denotes peptide-only
T91266 2747-2750 NN denotes map
T43073 2751-2759 NN denotes overlaid
T20774 2761-2766 JJ denotes Right
T74921 2767-2772 NN denotes panel
T5294 2772-2773 -COLON- denotes :
T27512 2774-2779 NN denotes SPARX
T17578 2780-2782 NN denotes 3D
T69974 2783-2794 NN denotes variability
T86316 2795-2801 NN denotes map51.
T39562 2802-2803 NN denotes b
T43304 2804-2808 JJ denotes Same
T52255 2809-2811 IN denotes as
T48004 2812-2814 IN denotes in
T51718 2815-2816 -LRB- denotes (
T36617 2816-2817 DT denotes a
T97382 2817-2818 -RRB- denotes )
T54597 2819-2822 CC denotes but
T81241 2823-2826 IN denotes for
T90782 2827-2832 NN denotes HIV-1
T13950 2833-2836 NNP denotes Env
T55209 2837-2842 NN denotes BG505
T53941 2843-2852 NN denotes SOSIP.664
T83312 2853-2862 NN denotes construct
T96415 2863-2865 IN denotes in
T45843 2866-2873 NN denotes complex
T56194 2874-2878 IN denotes with
T46276 2879-2884 CD denotes three
T95298 2885-2891 NNS denotes copies
T19490 2892-2894 IN denotes of
T71992 2895-2901 NN denotes RM20A3
T28802 2902-2915 JJ denotes base-specific
T65942 2916-2922 NN denotes Fabs51
R1378 T1363 T1360 arg2Of and,Visualising
R1379 T1363 T1361 arg1Of and,the
R1380 T1362 T1363 arg1Of HIV-1,and
R1381 T1366 T1363 arg2Of shields,and
R1382 T1366 T1364 arg1Of shields,SARS
R1383 T1366 T1365 arg1Of shields,glycan
R1384 T1363 T1367 arg1Of and,by
R1385 T1368 T1367 arg2Of cryo-EM,by
R40112 T3174 T8430 arg1Of Env,HIV-1
R77404 T3174 T27555 arg1Of Env,is
R67045 T80657 T27555 arg2Of protein,is
R19042 T80657 T55541 arg1Of protein,a
R70679 T80657 T20248 arg1Of protein,prototypic
R98963 T80657 T67286 arg1Of protein,viral
R51375 T80657 T69498 arg1Of protein,class
R65034 T80657 T3932 arg1Of protein,I
R38518 T80657 T49427 arg1Of protein,fusion
R18142 T80657 T46816 arg1Of protein,that
R95989 T80657 T99370 arg1Of protein,exhibits
R21203 T83381 T99370 arg2Of glycosylation,exhibits
R62409 T83381 T82158 arg1Of glycosylation,extensive
R45278 T83381 T40184 arg1Of glycosylation,surface
R36808 T99370 T34922 arg1Of exhibits,","
R25095 T99370 T41135 modOf exhibits,resulting
R66468 T41135 T52094 arg1Of resulting,in
R61128 T66049 T52094 arg2Of shield,in
R69033 T66049 T41086 arg1Of shield,an
R63943 T66049 T24478 arg1Of shield,effective
R16751 T66049 T12116 arg1Of shield,glycan
R91171 T80516 T24089 arg1Of aid,to
R35674 T41135 T24089 modOf resulting,to
R17624 T40146 T80516 arg2Of evasion,aid
R94826 T80516 T31245 arg1Of aid,from
R46405 T10989 T31245 arg2Of "response21,31",from
R49465 T10989 T10149 arg1Of "response21,31",the
R67827 T10989 T79574 arg1Of "response21,31",host
R10702 T10989 T93688 arg1Of "response21,31",adaptive
R76944 T10989 T94198 arg1Of "response21,31",immune
R87495 T89403 T32196 arg1Of used,In
R27221 T81817 T32196 arg2Of order,In
R83664 T52822 T32196 arg3Of visualize,In
R29301 T52822 T91723 arg1Of visualize,to
R70687 T26306 T52822 arg1Of we,visualize
R22808 T38040 T52822 arg2Of structure,visualize
R29213 T38040 T6796 arg1Of structure,the
R33103 T38040 T51236 arg1Of structure,of
R62729 T39465 T51236 arg2Of “shields”,of
R18785 T39465 T17574 arg1Of “shields”,the
R96799 T39465 T94895 arg1Of “shields”,respective
R10078 T39465 T2313 arg1Of “shields”,glycan
R37534 T39465 T63649 arg1Of “shields”,of
R43507 T65533 T63649 arg2Of coronavirus,of
R52525 T65533 T97323 arg1Of coronavirus,HIV-1
R22163 T97323 T48816 arg1Of HIV-1,and
R63270 T59243 T48816 arg2Of SARS,and
R44071 T65533 T59243 arg1Of coronavirus,SARS
R33310 T26306 T89403 arg1Of we,used
R15452 T27050 T89403 arg2Of microscopy,used
R76012 T27050 T31852 arg1Of microscopy,single-particle
R94625 T27050 T56676 arg1Of microscopy,cryo-electron
R52529 T27050 T97416 arg1Of microscopy,(
R80238 T56321 T97416 arg2Of cryo-EM,(
R68588 T61586 T97416 arg3Of ),(
R56245 T47125 T32555 arg1Of results,The
R84419 T47125 T36239 arg1Of results,for
R70463 T12931 T36239 arg2Of Env,for
R11834 T12931 T18889 arg1Of Env,HIV-1
R8425 T47125 T63067 arg1Of results,were
R65847 T30265 T63067 arg2Of reproduced,were
R18044 T47125 T30265 arg2Of results,reproduced
R87066 T30265 T57197 arg1Of reproduced,directly
R46593 T30265 T8292 arg1Of reproduced,from
R22503 T19388 T8292 arg2Of al.51,from
R33083 T37715 T31650 arg1Of et,Berndsen
R90854 T19388 T37715 arg1Of al.51,et
R2290 T30265 T9777 arg1Of reproduced,while
R26115 T72393 T9777 arg2Of reprocessed,while
R91746 T16458 T55752 arg1Of dataset52,the
R23575 T21233 T50993 arg1Of published,previously
R10375 T16458 T21233 arg1Of dataset52,published
R14263 T16458 T39264 arg1Of dataset52,SARS
R30163 T16458 T63581 arg1Of dataset52,2P
R49923 T16458 T19972 arg1Of dataset52,was
R47678 T72393 T19972 arg2Of reprocessed,was
R52503 T16458 T72393 arg2Of dataset52,reprocessed
R1686 T72393 T49131 arg1Of reprocessed,for
R55974 T69625 T49131 arg2Of study,for
R6998 T69625 T60843 arg1Of study,this
R67744 T46398 T12832 arg1Of were,Although
R43629 T32530 T12832 arg2Of are,Although
R1401 T29672 T24787 arg1Of datasets,cryo-EM
R89552 T29672 T9596 arg1Of datasets,of
R67665 T14676 T9596 arg2Of 53,of
R80940 T37894 T45576 arg1Of glycosylated,fully
R76365 T35124 T37894 arg1Of MERS,glycosylated
R75905 T35287 T35124 arg1Of virus,MERS
R59119 T35287 T87593 arg1Of virus,S41
R60460 T87593 T79382 arg1Of S41,and
R21732 T63281 T79382 arg2Of chimpanzee,and
R19327 T35287 T63281 arg1Of virus,chimpanzee
R8406 T35287 T35247 arg1Of virus,simian
R69725 T35287 T82138 arg1Of virus,immunodeficiency
R55541 T14676 T35287 arg1Of 53,virus
R62464 T35287 T14224 arg1Of virus,(
R13007 T81517 T14224 arg2Of SIVcpz,(
R57966 T3442 T14224 arg3Of ),(
R58028 T29672 T32530 arg1Of datasets,are
R4932 T95444 T32530 arg2Of available,are
R86107 T32530 T45598 arg1Of are,also
R62361 T29672 T95444 arg1Of datasets,available
R89109 T46398 T17171 arg1Of were,","
R65623 T37597 T88916 arg1Of data,only
R22986 T37597 T2700 arg1Of data,the
R34869 T37597 T19064 arg1Of data,HIV
R99409 T19064 T16401 arg1Of HIV,and
R21820 T74879 T16401 arg2Of SARS,and
R87987 T37597 T74879 arg1Of data,SARS
R84789 T37597 T46398 arg1Of data,were
R79506 T10901 T46398 arg2Of of,were
R74395 T37597 T10901 arg1Of data,of
R7658 T58744 T10901 arg2Of quality,of
R98976 T58744 T19935 arg1Of quality,sufficient
R4181 T58744 T47642 arg1Of quality,(
R34223 T27616 T47642 arg2Of Fig. 5,(
R6426 T15042 T47642 arg3Of ),(
R23813 T55283 T12200 arg1Of showed51,recently
R91435 T64790 T55283 arg1Of We,showed51
R40497 T63261 T55283 arg2Of leads,showed51
R90148 T63261 T5337 arg1Of leads,that
R54019 T85969 T15501 arg1Of dynamics,in
R94664 T11314 T15501 arg2Of Env,in
R43741 T11314 T81842 arg1Of Env,surface
R70932 T11314 T53947 arg2Of Env,exposed
R57155 T11314 T58293 arg1Of Env,glycans
R11772 T11314 T78469 arg1Of Env,HIV-1
R59703 T85969 T63261 arg1Of dynamics,leads
R6442 T63261 T50401 arg1Of leads,to
R58022 T26975 T50401 arg2Of network,to
R19289 T26975 T72222 arg1Of network,an
R58201 T26975 T69150 arg1Of network,extensive
R3033 T26975 T64977 arg1Of network,of
R14059 T71776 T64977 arg2Of interactions,of
R86686 T71776 T7784 arg1Of interactions,that
R47642 T71776 T35226 arg1Of interactions,drive
R48661 T34602 T35226 arg2Of structuring,drive
R6985 T34602 T68570 arg1Of structuring,higher-order
R73400 T34602 T35212 arg1Of structuring,in
R23718 T2686 T35212 arg2Of shield,in
R43138 T2686 T61552 arg1Of shield,the
R16504 T2686 T88226 arg1Of shield,glycan
R91717 T49009 T70456 arg1Of structure,This
R60972 T49009 T80667 arg1Of structure,defines
R5536 T1508 T80667 arg2Of boundaries,defines
R14014 T1508 T33829 arg1Of boundaries,diffuse
R71165 T1508 T66208 arg1Of boundaries,between
R84605 T66804 T66208 arg2Of surface,between
R36824 T66804 T95551 arg2Of surface,buried
R6781 T66804 T27513 arg1Of surface,and
R13511 T66804 T63689 arg2Of surface,exposed
R42837 T66804 T23712 arg1Of surface,surface
R35366 T66804 T90175 arg1Of surface,protein
R40133 T66804 T71072 arg1Of surface,","
R67428 T66804 T80348 arg1Of surface,which
R19941 T66804 T9316 arg1Of surface,can
R75191 T90504 T9316 arg2Of serve,can
R68916 T66804 T90504 arg1Of surface,serve
R85823 T69932 T90504 arg2Of define,serve
R15048 T69932 T42110 arg1Of define,to
R88756 T66804 T69932 arg1Of surface,define
R66006 T2204 T69932 arg2Of sites,define
R13031 T2204 T67682 arg1Of sites,potential
R31526 T2204 T70578 arg1Of sites,of
R46771 T95274 T70578 arg2Of vulnerability,of
R61420 T46703 T30395 arg1Of Cryo-EM,captures
R99133 T43250 T30395 arg2Of results,captures
R15252 T7879 T87072 arg1Of structure,the
R72204 T7879 T44958 arg1Of structure,ensemble-average
R1794 T7879 T75651 arg1Of structure,of
R85584 T73691 T75651 arg2Of and,of
R44731 T66273 T73691 arg1Of biomolecules,and
R32592 T11220 T73691 arg2Of dynamics,and
R16052 T11220 T31109 arg1Of dynamics,therefore
R8839 T11220 T12255 arg1Of dynamics,glycan
R58120 T7879 T43250 arg1Of structure,results
R43360 T43250 T52169 arg1Of results,in
R76821 T49153 T52169 arg2Of density,in
R66611 T49153 T64021 arg2Of density,blurred
R48079 T43250 T2441 arg1Of results,at
R30996 T16085 T2441 arg2Of resolutions,at
R8253 T16085 T80700 arg1Of resolutions,the
R32137 T16085 T86172 arg1Of resolutions,necessary
R99471 T86172 T28589 arg1Of necessary,for
R98814 T42839 T28589 arg2Of building,for
R66350 T43748 T42839 arg2Of structure,building
R32590 T43748 T3599 arg1Of structure,atomic
R24318 T94206 T10071 arg1Of showed,However
R26175 T94206 T88433 arg1Of showed,","
R53086 T97506 T94206 arg1Of we,showed
R62847 T91691 T94206 arg2Of how,showed
R2380 T70541 T91691 arg1Of and,how
R23756 T89162 T17411 arg1Of as,a
R55557 T82430 T2527 arg1Of combination,simple
R59136 T82430 T32469 arg1Of combination,of
R91541 T10413 T32469 arg2Of and,of
R34127 T93291 T40028 arg1Of filtering,low-pass
R99542 T93291 T10413 arg1Of filtering,and
R31235 T2487 T10413 arg2Of auto-thresholding,and
R21549 T89162 T78379 arg1Of as,","
R94567 T89162 T27010 arg1Of as,as
R56677 T89162 T32044 arg1Of as,well
R84025 T82430 T89162 arg1Of combination,as
R77886 T14190 T89162 arg2Of analysis,as
R74774 T14190 T8187 arg1Of analysis,3D
R32077 T14190 T99213 arg1Of analysis,variability
R45513 T70541 T81037 arg1Of and,","
R52288 T89162 T87732 arg1Of as,can
R85159 T70541 T87732 arg2Of and,can
R23242 T89162 T9264 arg1Of as,reveal
R90965 T31709 T9264 arg2Of structure,reveal
R30322 T31709 T36472 arg1Of structure,the
R11789 T31709 T15866 arg1Of structure,previously
R87205 T31709 T33845 arg2Of structure,hidden
R9606 T31709 T97881 arg1Of structure,of
R67400 T15037 T97881 arg2Of shield,of
R54575 T15037 T77189 arg1Of shield,the
R61674 T15037 T22984 arg1Of shield,SARS
R67642 T15037 T32877 arg1Of shield,glycan
R16567 T9264 T70541 arg1Of reveal,and
R41315 T30415 T70541 arg2Of compare,and
R38659 T89162 T30415 arg1Of as,compare
R40791 T37461 T30415 arg2Of it,compare
R83994 T30415 T52236 arg1Of compare,with
R97825 T3337 T52236 arg2Of shield51,with
R73479 T3337 T25513 arg1Of shield51,the
R23692 T3337 T63380 arg1Of shield51,HIV-1
R50639 T3337 T80636 arg1Of shield51,Env
R28975 T3337 T69159 arg1Of shield51,glycan
R5473 T3337 T64033 arg1Of shield51,(
R8522 T94502 T64033 arg2Of Fig. 5,(
R58315 T94581 T64033 arg3Of ),(
R57363 T60289 T75223 arg1Of We,observe
R66074 T99824 T75223 arg2Of density,observe
R81587 T99824 T57545 arg1Of density,the
R35059 T87308 T48330 arg1Of all-encompassing,nearly
R7274 T99824 T87308 arg1Of density,all-encompassing
R88937 T99824 T1558 arg1Of density,glycan
R66924 T99824 T59798 arg1Of density,on
R61464 T33263 T59798 arg2Of and,on
R83562 T14383 T56235 arg1Of Env,HIV-1
R85086 T14383 T33263 arg1Of Env,and
R78120 T4213 T33263 arg2Of evidence,and
R42903 T33263 T91161 arg1Of and,for
R57290 T48593 T91161 arg2Of interactions,for
R88967 T48593 T79082 arg1Of interactions,extensive
R10709 T48593 T66189 arg1Of interactions,glycan–glycan
R45240 T99824 T42535 arg1Of density,","
R16806 T44869 T14663 arg1Of in,especially
R95483 T99824 T44869 arg1Of density,in
R56293 T20998 T44869 arg2Of regions,in
R89068 T20998 T77065 arg1Of regions,the
R85023 T20998 T90752 arg1Of regions,oligomannose
R14595 T20998 T24864 arg1Of regions,patch
R53601 T69929 T55492 arg1Of whereas,","
R41847 T75223 T69929 arg1Of observe,whereas
R72281 T67487 T69929 arg2Of and,whereas
R41117 T59031 T90575 arg1Of glycans,the
R11577 T59031 T94235 arg1Of glycans,on
R76941 T7541 T94235 arg2Of S,on
R61132 T7541 T22232 arg1Of S,SARS
R12423 T59031 T66013 arg1Of glycans,appear
R21940 T7370 T66013 arg2Of isolated,appear
R42488 T7370 T27090 arg1Of isolated,more
R49214 T59031 T7370 arg1Of glycans,isolated
R75703 T66013 T67487 arg1Of appear,and
R14857 T50530 T67487 arg2Of lack,and
R31178 T59031 T50530 arg1Of glycans,lack
R58449 T80844 T50530 arg2Of networks,lack
R18453 T80844 T21892 arg1Of networks,the
R78728 T80844 T55852 arg1Of networks,wide-ranging
R63082 T80844 T70160 arg1Of networks,glycan
R85815 T80844 T83936 arg1Of networks,that
R62340 T80844 T81018 arg1Of networks,are
R32364 T82951 T81018 arg2Of hallmark,are
R56572 T82951 T68036 arg1Of hallmark,the
R69107 T82951 T16903 arg1Of hallmark,of
R36848 T57983 T16903 arg2Of "shield54,55",of
R53995 T57983 T2902 arg1Of "shield54,55",an
R40757 T57983 T18742 arg1Of "shield54,55",effective
R23595 T57983 T88640 arg1Of "shield54,55",glycan
R22476 T79677 T96638 arg1Of maps,The
R95997 T79677 T9355 arg1Of maps,3D
R80519 T79677 T47791 arg1Of maps,variability
R40472 T79677 T51290 arg1Of maps,are
R82084 T28675 T51290 arg2Of sensitive,are
R56965 T28675 T66740 arg1Of sensitive,more
R45386 T79677 T28675 arg1Of maps,sensitive
R87747 T28675 T51626 arg1Of sensitive,to
R64143 T42122 T51626 arg2Of signal,to
R50005 T42122 T96563 arg1Of signal,low
R94025 T42122 T5756 arg1Of signal,intensity
R70972 T51290 T93380 arg1Of are,and
R95204 T52275 T93380 arg2Of reveal,and
R58754 T79677 T52275 arg1Of maps,reveal
R14145 T18648 T52275 arg2Of interactions,reveal
R5294 T18648 T65761 arg1Of interactions,additional
R68909 T18648 T40659 arg1Of interactions,glycan–glycan
R88310 T52275 T53697 arg1Of reveal,in
R42132 T61777 T53697 arg2Of maps,in
R18814 T61777 T13379 arg1Of maps,both
R35607 T93380 T1991 arg1Of and,","
R8195 T3893 T1991 arg2Of shown,","
R90057 T3893 T10706 arg1Of shown,however
R82099 T67026 T21547 arg1Of domains,the
R27746 T67026 T89902 arg1Of domains,S1
R92599 T67026 T24397 arg1Of domains,receptor-binding
R73569 T67026 T98351 arg1Of domains,in
R45720 T19203 T98351 arg2Of dataset,in
R30503 T19203 T69700 arg1Of dataset,the
R24149 T19203 T97210 arg1Of dataset,SARS
R20104 T67026 T21495 arg1Of domains,were
R88806 T3893 T21495 arg2Of shown,were
R56386 T67026 T3893 arg2Of domains,shown
R54479 T68704 T3893 arg3Of exist,shown
R65901 T68704 T33461 arg1Of exist,to
R89466 T67026 T68704 arg1Of domains,exist
R55901 T68704 T1970 arg1Of exist,in
R71972 T75781 T1970 arg2Of up,in
R75698 T75781 T91066 arg1Of up,both
R54454 T1970 T44006 arg1Of in,and
R77813 T47879 T44006 arg2Of down,and
R6563 T68704 T47879 arg1Of exist,down
R57265 T22009 T47879 arg2Of conformations52,down
R54511 T3893 T80149 arg1Of shown,","
R68204 T3893 T10724 modOf shown,leading
R29757 T10724 T29355 arg1Of leading,to
R87860 T15044 T29355 arg2Of and,to
R58772 T15651 T48291 arg1Of resolution,poor
R20667 T15651 T15044 arg1Of resolution,and
R82833 T78120 T15044 arg2Of 2D-variability,and
R22945 T78120 T36313 arg1Of 2D-variability,significant
R38420 T15044 T97054 arg1Of and,which
R98282 T15044 T80897 arg1Of and,is
R52865 T73857 T80897 arg2Of convolved,is
R73995 T15044 T73857 arg2Of and,convolved
R3618 T73857 T52453 arg1Of convolved,with
R59937 T9415 T52453 arg2Of variability,with
R49442 T91463 T52453 arg3Of coming,with
R80207 T9415 T12417 arg1Of variability,the
R34571 T9415 T91463 arg1Of variability,coming
R6872 T91463 T37758 arg1Of coming,from
R43624 T69399 T37758 arg2Of glycans,from
R98318 T73857 T37469 arg1Of convolved,and
R66138 T7534 T37469 arg2Of limits,and
R77790 T15044 T7534 arg1Of and,limits
R83430 T16169 T7534 arg2Of interpretability,limits
R17631 T16169 T29335 arg1Of interpretability,the
R1774 T16169 T54909 arg1Of interpretability,of
R57067 T73688 T54909 arg2Of effects,of
R86812 T73688 T36751 arg1Of effects,glycan
R74249 T73688 T68517 arg1Of effects,shielding
R94853 T7534 T27520 arg1Of limits,in
R81871 T15004 T27520 arg2Of region,in
R64817 T15004 T1634 arg1Of region,this
R92714 T15004 T14842 arg1Of region,of
R8559 T85741 T14842 arg2Of map,of
R44147 T85741 T18381 arg1Of map,the
R35005 T19047 T77710 arg1Of analysis,Fig.
R38678 T77710 T43639 arg1Of Fig.,5
R99431 T19047 T80136 arg1Of analysis,Comparative
R13336 T19047 T57723 arg1Of analysis,cryo-EM
R99511 T19047 T52944 arg1Of analysis,of
R26999 T87387 T52944 arg2Of and,of
R12478 T71022 T86979 arg1Of S,SARS
R9050 T71022 T87387 arg1Of S,and
R91871 T21302 T87387 arg2Of shields,and
R77760 T21302 T92374 arg1Of shields,HIV-1
R2872 T21302 T58960 arg1Of shields,Env
R23954 T21302 T67673 arg1Of shields,glycan
R98907 T16113 T48820 arg1Of panel,a
R90546 T16113 T79466 arg1Of panel,Left
R66182 T16113 T98169 arg1Of panel,:
R45510 T56273 T63629 arg2Of map,Sharpened
R28106 T56273 T90429 arg1Of map,3.2-Å-resolution
R92380 T56273 T6423 arg1Of map,C3-symmetric
R65018 T56273 T13124 arg1Of map,cryo-EM
R80721 T56273 T86558 arg1Of map,of
R26733 T75209 T86558 arg2Of ectodomain52,of
R61425 T84496 T37174 arg1Of S,SARS
R9682 T75209 T84496 arg1Of ectodomain52,S
R64810 T75209 T86959 arg1Of ectodomain52,2P
R88141 T75209 T37067 arg2Of ectodomain52,visualized
R95052 T37067 T22530 arg1Of visualized,at
R74218 T58510 T22530 arg2Of level,at
R4190 T58510 T60171 arg1Of level,a
R55817 T58510 T27128 arg1Of level,high
R67792 T58510 T94740 arg1Of level,contour
R69414 T56273 T66412 arg1Of map,with
R80505 T68442 T66412 arg2Of domains,with
R23158 T68442 T32176 arg2Of domains,disordered
R42599 T68442 T5395 arg1Of domains,S1
R30349 T68442 T34000 arg1Of domains,receptor-binding
R77410 T34000 T54890 arg1Of receptor-binding,and
R20022 T9018 T54890 arg2Of N-terminal,and
R45262 T68442 T9018 arg1Of domains,N-terminal
R46136 T68442 T72184 arg1Of domains,extending
R54218 T72184 T12801 arg1Of extending,out
R98187 T72184 T26493 arg1Of extending,from
R88765 T39891 T26493 arg2Of core,from
R79877 T39891 T4854 arg1Of core,the
R58999 T39891 T35333 arg1Of core,central
R3609 T40721 T4786 arg1Of panel,Middle
R2263 T40721 T2753 arg1Of panel,:
R7635 T90188 T68941 arg1Of map,Low-pass
R50307 T90188 T98545 arg1Of map,filtered
R44751 T90188 T5712 arg1Of map,(
R94760 T65635 T5712 arg2Of lpf,(
R81995 T36825 T5712 arg3Of ),(
R54195 T90188 T66628 arg1Of map,cryo-EM
R93131 T90188 T57750 arg1Of map,of
R32904 T69826 T57750 arg2Of glycoprotein,of
R22697 T69826 T25808 arg1Of glycoprotein,the
R67130 T69826 T87240 arg2Of glycoprotein,visualised
R62598 T87240 T62278 arg1Of visualised,at
R52700 T68027 T62278 arg2Of level,at
R84135 T68027 T88612 arg1Of level,a
R86475 T68027 T55069 arg1Of level,low
R91771 T68027 T38898 arg1Of level,contour
R27443 T22579 T69920 arg1Of with,along
R76131 T87240 T22579 arg1Of visualised,with
R74494 T43073 T22579 arg2Of overlaid,with
R82819 T43073 T51416 arg1Of overlaid,a
R67128 T43073 T26917 arg1Of overlaid,simulated
R3623 T43073 T72481 arg1Of overlaid,peptide-only
R82360 T43073 T91266 arg1Of overlaid,map
R36912 T74921 T20774 arg1Of panel,Right
R76910 T74921 T5294 arg1Of panel,:
R33651 T39562 T5294 arg2Of b,:
R13725 T39562 T27512 arg1Of b,SPARX
R86604 T39562 T17578 arg1Of b,3D
R27480 T39562 T69974 arg1Of b,variability
R10741 T39562 T86316 arg1Of b,map51.
R48535 T5294 T43304 arg1Of :,Same
R76558 T48004 T52255 arg1Of in,as
R21082 T43304 T48004 arg1Of Same,in
R71256 T83312 T48004 arg2Of construct,in
R28363 T83312 T51718 arg1Of construct,(
R62327 T83312 T36617 arg1Of construct,a
R96993 T53941 T97382 arg1Of SOSIP.664,)
R86109 T53941 T54597 arg1Of SOSIP.664,but
R85461 T53941 T81241 arg1Of SOSIP.664,for
R47042 T53941 T90782 arg1Of SOSIP.664,HIV-1
R58191 T53941 T13950 arg1Of SOSIP.664,Env
R84719 T53941 T55209 arg1Of SOSIP.664,BG505
R63284 T83312 T53941 arg1Of construct,SOSIP.664
R55994 T83312 T96415 arg1Of construct,in
R42276 T45843 T96415 arg2Of complex,in
R52712 T45843 T56194 arg1Of complex,with
R83415 T95298 T56194 arg2Of copies,with
R90004 T95298 T46276 arg1Of copies,three
R72441 T95298 T19490 arg1Of copies,of
R77147 T65942 T19490 arg2Of Fabs51,of
R10660 T65942 T71992 arg1Of Fabs51,RM20A3
R35471 T65942 T28802 arg1Of Fabs51,base-specific

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T98 16-19 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T99 57-60 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T100 104-111 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T101 333-336 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T102 436-439 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T103 717-720 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T104 834-837 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T105 1025-1032 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T106 1501-1504 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T107 1594-1597 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T108 2303-2306 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T109 2358-2361 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T110 2446-2449 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T111 2653-2656 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T112 2664-2676 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T113 2747-2750 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T114 2827-2830 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T135 104-111 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T136 826-833 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T137 1025-1032 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T138 1717-1724 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T139 2213-2220 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T140 2664-2676 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T141 2734-2741 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T122 16-21 Species denotes HIV-1 NCBItxid:11676
T123 26-30 Species denotes SARS NCBItxid:694009
T124 57-62 Species denotes HIV-1 NCBItxid:11676
T125 333-338 Species denotes HIV-1 NCBItxid:11676
T126 343-359 Species denotes SARS coronavirus NCBItxid:694009
T127 343-347 Species denotes SARS NCBItxid:694009
T128 436-441 Species denotes HIV-1 NCBItxid:11676
T129 525-529 Species denotes SARS NCBItxid:694009
T130 623-627 Species denotes MERS NCBItxid:1335626
T131 636-646 Species denotes chimpanzee NCBItxid:9598
T132 647-676 Species denotes simian immunodeficiency virus NCBItxid:11723
T133 678-684 Species denotes SIVcpz NCBItxid:388909
T134 717-720 Species denotes HIV NCBItxid:57667|NCBItxid:35274|NCBItxid:12721|NCBItxid:11709|NCBItxid:11676
T139 725-729 Species denotes SARS NCBItxid:694009
T140 834-839 Species denotes HIV-1 NCBItxid:11676
T141 1458-1462 Species denotes SARS NCBItxid:694009
T142 1501-1506 Species denotes HIV-1 NCBItxid:11676
T143 1594-1599 Species denotes HIV-1 NCBItxid:11676
T144 1728-1732 Species denotes SARS NCBItxid:694009
T145 2033-2037 Species denotes SARS NCBItxid:694009
T146 2347-2351 Species denotes SARS NCBItxid:694009
T147 2358-2363 Species denotes HIV-1 NCBItxid:11676
T148 2453-2457 Species denotes SARS NCBItxid:694009
T149 2827-2832 Species denotes HIV-1 NCBItxid:11676

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T102 0-56 Sentence denotes Visualising the HIV-1 and SARS glycan shields by cryo-EM
T103 57-258 Sentence denotes HIV-1 Env is a prototypic viral class I fusion protein that exhibits extensive surface glycosylation, resulting in an effective glycan shield to aid evasion from the host adaptive immune response21,31.
T104 259-419 Sentence denotes In order to visualize the structure of the respective glycan “shields” of HIV-1 and SARS coronavirus we used single-particle cryo-electron microscopy (cryo-EM).
T105 420-574 Sentence denotes The results for HIV-1 Env were reproduced directly from Berndsen et al.51 while the previously published SARS 2P dataset52 was reprocessed for this study.
T106 575-771 Sentence denotes Although cryo-EM datasets of fully glycosylated MERS S41 and chimpanzee simian immunodeficiency virus (SIVcpz)53 are also available, only the HIV and SARS data were of sufficient quality (Fig. 5).
T107 772-947 Sentence denotes We recently showed51 that dynamics in surface exposed glycans HIV-1 Env leads to an extensive network of interactions that drive higher-order structuring in the glycan shield.
T108 948-1101 Sentence denotes This structure defines diffuse boundaries between buried and exposed surface protein surface, which can serve to define potential sites of vulnerability.
T109 1102-1282 Sentence denotes Cryo-EM captures the ensemble-average structure of biomolecules and therefore glycan dynamics results in blurred density at the resolutions necessary for building atomic structure.
T110 1283-1536 Sentence denotes However, we showed how a simple combination of low-pass filtering and auto-thresholding, as well as 3D variability analysis, can reveal the previously hidden structure of the SARS glycan shield and compare it with the HIV-1 Env glycan shield51 (Fig. 5).
T111 1537-1855 Sentence denotes We observe the nearly all-encompassing glycan density on HIV-1 Env and evidence for extensive glycan–glycan interactions, especially in the oligomannose patch regions, whereas the glycans on SARS S appear more isolated and lack the wide-ranging glycan networks that are the hallmark of an effective glycan shield54,55.
T112 1856-2307 Sentence denotes The 3D variability maps are more sensitive to low intensity signal and reveal additional glycan–glycan interactions in both maps, however the S1 receptor-binding domains in the SARS dataset were shown to exist in both up and down conformations52, leading to poor resolution and significant 2D-variability which is convolved with the variability coming from glycans and limits the interpretability of glycan shielding effects in this region of the map.
T113 2308-2383 Sentence denotes Fig. 5 Comparative cryo-EM analysis of SARS S and HIV-1 Env glycan shields.
T114 2384-2397 Sentence denotes a Left panel:
T115 2398-2606 Sentence denotes Sharpened 3.2-Å-resolution C3-symmetric cryo-EM map of SARS S 2P ectodomain52 visualized at a high contour level with disordered S1 receptor-binding and N-terminal domains extending out from the central core.
T116 2607-2620 Sentence denotes Middle panel:
T117 2621-2760 Sentence denotes Low-pass filtered (lpf) cryo-EM map of the glycoprotein visualised at a low contour level along with a simulated peptide-only map overlaid.
T118 2761-2923 Sentence denotes Right panel: SPARX 3D variability map51. b Same as in (a) but for HIV-1 Env BG505 SOSIP.664 construct in complex with three copies of RM20A3 base-specific Fabs51.

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T59 26-30 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T60 343-347 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T61 525-529 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T62 654-670 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T63 725-729 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T64 1458-1462 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T65 1728-1732 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 2033-2037 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 2347-2351 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T68 2453-2457 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
601 16-21 Species denotes HIV-1 Tax:11676
603 26-30 Disease denotes SARS MESH:D045169
602 31-37 Chemical denotes glycan MESH:D011134
661 57-62 Species denotes HIV-1 Tax:11676
656 63-66 Gene denotes Env Gene:64006
671 185-191 Chemical denotes glycan MESH:D011134
672 313-319 Chemical denotes glycan MESH:D011134
662 333-338 Species denotes HIV-1 Tax:11676
663 343-359 Species denotes SARS coronavirus Tax:694009
664 436-441 Species denotes HIV-1 Tax:11676
657 442-445 Gene denotes Env Gene:64006
665 525-531 Species denotes SARS 2 Tax:2697049
689 623-627 Disease denotes MERS MESH:D018352
666 636-646 Species denotes chimpanzee Tax:9598
667 647-685 Species denotes simian immunodeficiency virus (SIVcpz) Tax:11723
690 725-729 Disease denotes SARS MESH:D045169
673 826-833 Chemical denotes glycans MESH:D011134
668 834-839 Species denotes HIV-1 Tax:11676
658 840-843 Gene denotes Env Gene:64006
674 933-939 Chemical denotes glycan MESH:D011134
675 1180-1186 Chemical denotes glycan MESH:D011134
691 1458-1462 Disease denotes SARS MESH:D045169
676 1463-1469 Chemical denotes glycan MESH:D011134
669 1501-1506 Species denotes HIV-1 Tax:11676
659 1507-1510 Gene denotes Env Gene:64006
677 1511-1517 Chemical denotes glycan MESH:D011134
678 1576-1582 Chemical denotes glycan MESH:D011134
670 1594-1599 Species denotes HIV-1 Tax:11676
660 1600-1603 Gene denotes Env Gene:64006
679 1631-1637 Chemical denotes glycan MESH:D011134
680 1638-1644 Chemical denotes glycan MESH:D011134
681 1677-1689 Chemical denotes oligomannose
682 1717-1724 Chemical denotes glycans MESH:D011134
692 1728-1732 Disease denotes SARS MESH:D045169
683 1782-1788 Chemical denotes glycan MESH:D011134
684 1836-1842 Chemical denotes glycan MESH:D011134
685 1945-1951 Chemical denotes glycan MESH:D011134
686 1952-1958 Chemical denotes glycan MESH:D011134
693 2033-2037 Disease denotes SARS MESH:D045169
687 2213-2220 Chemical denotes glycans MESH:D011134
688 2256-2262 Chemical denotes glycan MESH:D011134
611 2347-2351 Disease denotes SARS MESH:D045169
609 2358-2363 Species denotes HIV-1 Tax:11676
608 2364-2367 Gene denotes Env Gene:64006
610 2368-2374 Chemical denotes glycan MESH:D011134
617 2453-2457 Disease denotes SARS MESH:D045169
616 2827-2832 Species denotes HIV-1 Tax:11676
615 2833-2836 Gene denotes Env Gene:64006

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T3769 63-66 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3771 442-445 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3773 840-843 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3775 1017-1032 Protein denotes surface protein https://www.uniprot.org/uniprot/V9GXQ5|https://www.uniprot.org/uniprot/Q9YWM3|https://www.uniprot.org/uniprot/Q9YNA9|https://www.uniprot.org/uniprot/Q9YNA7|https://www.uniprot.org/uniprot/Q9YNA5|https://www.uniprot.org/uniprot/Q9UQF0|https://www.uniprot.org/uniprot/Q9UNM3|https://www.uniprot.org/uniprot/Q9UKH3|https://www.uniprot.org/uniprot/Q9UBU4|https://www.uniprot.org/uniprot/Q9TTC0|https://www.uniprot.org/uniprot/Q9QC06|https://www.uniprot.org/uniprot/Q9NZG3|https://www.uniprot.org/uniprot/Q9NX77|https://www.uniprot.org/uniprot/Q9NRZ2|https://www.uniprot.org/uniprot/Q9N2K0|https://www.uniprot.org/uniprot/Q9N2J8|https://www.uniprot.org/uniprot/Q9IZT0|https://www.uniprot.org/uniprot/Q96PI6|https://www.uniprot.org/uniprot/Q96PI3|https://www.uniprot.org/uniprot/Q96L63|https://www.uniprot.org/uniprot/Q902F9|https://www.uniprot.org/uniprot/Q902F8|https://www.uniprot.org/uniprot/Q8TD93|https://www.uniprot.org/uniprot/Q8NHY7|https://www.uniprot.org/uniprot/Q8MIB6|https://www.uniprot.org/uniprot/Q8BI41|https://www.uniprot.org/uniprot/Q89529|https://www.uniprot.org/uniprot/Q88938|https://www.uniprot.org/uniprot/Q87041|https://www.uniprot.org/uniprot/Q86355|https://www.uniprot.org/uniprot/Q85646|https://www.uniprot.org/uniprot/Q85629|https://www.uniprot.org/uniprot/Q85628|https://www.uniprot.org/uniprot/Q85517|https://www.uniprot.org/uniprot/Q85516|https://www.uniprot.org/uniprot/Q85515|https://www.uniprot.org/uniprot/Q85501|https://www.uniprot.org/uniprot/Q85500|https://www.uniprot.org/uniprot/Q85489|https://www.uniprot.org/uniprot/Q85488|https://www.uniprot.org/uniprot/Q82857|https://www.uniprot.org/uniprot/Q811N4|https://www.uniprot.org/uniprot/Q811M9|https://www.uniprot.org/uniprot/Q80SY1|https://www.uniprot.org/uniprot/Q80SY0|https://www.uniprot.org/uniprot/Q80SW8|https://www.uniprot.org/uniprot/Q80SW7|https://www.uniprot.org/uniprot/Q78N94|https://www.uniprot.org/uniprot/Q78N73|https://www.uniprot.org/uniprot/Q78N71|https://www.uniprot.org/uniprot/P60507|https://www.uniprot.org/uniprot/P51520|https://www.uniprot.org/uniprot/P51519|https://www.uniprot.org/uniprot/P51515|https://www.uniprot.org/uniprot/P35954|https://www.uniprot.org/uniprot/P33498|https://www.uniprot.org/uniprot/P32541|https://www.uniprot.org/uniprot/P31796|https://www.uniprot.org/uniprot/P31794|https://www.uniprot.org/uniprot/P31791|https://www.uniprot.org/uniprot/P31789|https://www.uniprot.org/uniprot/P31627|https://www.uniprot.org/uniprot/P31626|https://www.uniprot.org/uniprot/P31621|https://www.uniprot.org/uniprot/P27399|https://www.uniprot.org/uniprot/P26804|https://www.uniprot.org/uniprot/P26803|https://www.uniprot.org/uniprot/P25507|https://www.uniprot.org/uniprot/P25506|https://www.uniprot.org/uniprot/P25505|https://www.uniprot.org/uniprot/P25504|https://www.uniprot.org/uniprot/P25057|https://www.uniprot.org/uniprot/P23423|https://www.uniprot.org/uniprot/P23422|https://www.uniprot.org/uniprot/P23073|https://www.uniprot.org/uniprot/P23064|https://www.uniprot.org/uniprot/P22430|https://www.uniprot.org/uniprot/P22429|https://www.uniprot.org/uniprot/P22428|https://www.uniprot.org/uniprot/P22427|https://www.uniprot.org/uniprot/P21446|https://www.uniprot.org/uniprot/P21445|https://www.uniprot.org/uniprot/P21444|https://www.uniprot.org/uniprot/P21443|https://www.uniprot.org/uniprot/P21436|https://www.uniprot.org/uniprot/P21415|https://www.uniprot.org/uniprot/P21412|https://www.uniprot.org/uniprot/P19557|https://www.uniprot.org/uniprot/P19556|https://www.uniprot.org/uniprot/P19030|https://www.uniprot.org/uniprot/P16899|https://www.uniprot.org/uniprot/P16090|https://www.uniprot.org/uniprot/P16082|https://www.uniprot.org/uniprot/P15073|https://www.uniprot.org/uniprot/P14351|https://www.uniprot.org/uniprot/P14075|https://www.uniprot.org/uniprot/P11306|https://www.uniprot.org/uniprot/P11268|https://www.uniprot.org/uniprot/P11261|https://www.uniprot.org/uniprot/P10404|https://www.uniprot.org/uniprot/P10269|https://www.uniprot.org/uniprot/P10259|https://www.uniprot.org/uniprot/P0C212|https://www.uniprot.org/uniprot/P08360|https://www.uniprot.org/uniprot/P08359|https://www.uniprot.org/uniprot/P07575|https://www.uniprot.org/uniprot/P06752|https://www.uniprot.org/uniprot/P06751|https://www.uniprot.org/uniprot/P06445|https://www.uniprot.org/uniprot/P04502|https://www.uniprot.org/uniprot/P04027|https://www.uniprot.org/uniprot/P03399|https://www.uniprot.org/uniprot/P03397|https://www.uniprot.org/uniprot/P03396|https://www.uniprot.org/uniprot/P03395|https://www.uniprot.org/uniprot/P03392|https://www.uniprot.org/uniprot/P03391|https://www.uniprot.org/uniprot/P03390|https://www.uniprot.org/uniprot/P03388|https://www.uniprot.org/uniprot/P03387|https://www.uniprot.org/uniprot/P03386|https://www.uniprot.org/uniprot/P03385|https://www.uniprot.org/uniprot/P03383|https://www.uniprot.org/uniprot/P03382|https://www.uniprot.org/uniprot/P03381|https://www.uniprot.org/uniprot/P03380|https://www.uniprot.org/uniprot/P03379|https://www.uniprot.org/uniprot/P03374|https://www.uniprot.org/uniprot/O95280|https://www.uniprot.org/uniprot/O95245|https://www.uniprot.org/uniprot/O95244|https://www.uniprot.org/uniprot/O71037|https://www.uniprot.org/uniprot/O56861|https://www.uniprot.org/uniprot/O42043|https://www.uniprot.org/uniprot/O00354|https://www.uniprot.org/uniprot/I7GPQ9|https://www.uniprot.org/uniprot/B2RPD4|https://www.uniprot.org/uniprot/A8K9G3|https://www.uniprot.org/uniprot/A1Z653|https://www.uniprot.org/uniprot/Q77YG8|https://www.uniprot.org/uniprot/Q77YG4|https://www.uniprot.org/uniprot/Q69386|https://www.uniprot.org/uniprot/Q69384|https://www.uniprot.org/uniprot/Q65597|https://www.uniprot.org/uniprot/Q64984|https://www.uniprot.org/uniprot/Q5JTS0|https://www.uniprot.org/uniprot/Q5G5D5|https://www.uniprot.org/uniprot/Q2XSV0|https://www.uniprot.org/uniprot/Q2F7J1|https://www.uniprot.org/uniprot/Q2F7I8|https://www.uniprot.org/uniprot/Q28416|https://www.uniprot.org/uniprot/Q27ID8|https://www.uniprot.org/uniprot/Q14264|https://www.uniprot.org/uniprot/Q0R5Q9|https://www.uniprot.org/uniprot/Q09SZ7|https://www.uniprot.org/uniprot/Q05312|https://www.uniprot.org/uniprot/Q04995|https://www.uniprot.org/uniprot/Q04993|https://www.uniprot.org/uniprot/Q03817|https://www.uniprot.org/uniprot/Q03816|https://www.uniprot.org/uniprot/Q03804|https://www.uniprot.org/uniprot/Q03803|https://www.uniprot.org/uniprot/Q02282|https://www.uniprot.org/uniprot/Q02077|https://www.uniprot.org/uniprot/Q02076|https://www.uniprot.org/uniprot/P90288|https://www.uniprot.org/uniprot/P61570|https://www.uniprot.org/uniprot/P61567|https://www.uniprot.org/uniprot/P61566|https://www.uniprot.org/uniprot/P61565|https://www.uniprot.org/uniprot/P61564|https://www.uniprot.org/uniprot/P61563|https://www.uniprot.org/uniprot/P61562|https://www.uniprot.org/uniprot/P61561|https://www.uniprot.org/uniprot/P61559|https://www.uniprot.org/uniprot/P61558|https://www.uniprot.org/uniprot/P61557|https://www.uniprot.org/uniprot/P61556|https://www.uniprot.org/uniprot/P61555|https://www.uniprot.org/uniprot/P61554|https://www.uniprot.org/uniprot/P61553|https://www.uniprot.org/uniprot/P61552|https://www.uniprot.org/uniprot/P61550|https://www.uniprot.org/uniprot/P60608|https://www.uniprot.org/uniprot/P60508
T3960 1507-1510 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3962 1600-1603 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3964 2364-2367 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3966 2664-2676 Protein denotes glycoprotein https://www.uniprot.org/uniprot/Q9QSP1|https://www.uniprot.org/uniprot/Q9QJT6|https://www.uniprot.org/uniprot/Q9JGT4|https://www.uniprot.org/uniprot/Q9IPJ6|https://www.uniprot.org/uniprot/Q9DIC6|https://www.uniprot.org/uniprot/Q91DS0|https://www.uniprot.org/uniprot/Q91C28|https://www.uniprot.org/uniprot/Q8QQA2|https://www.uniprot.org/uniprot/Q8QPE5|https://www.uniprot.org/uniprot/Q8QPE4|https://www.uniprot.org/uniprot/Q8QPE3|https://www.uniprot.org/uniprot/Q8JTH0|https://www.uniprot.org/uniprot/Q8BDV6|https://www.uniprot.org/uniprot/Q8B6J6|https://www.uniprot.org/uniprot/Q8B0I1|https://www.uniprot.org/uniprot/Q8B0H6|https://www.uniprot.org/uniprot/Q8B0H1|https://www.uniprot.org/uniprot/Q89669|https://www.uniprot.org/uniprot/Q85213|https://www.uniprot.org/uniprot/Q82706|https://www.uniprot.org/uniprot/Q82683|https://www.uniprot.org/uniprot/Q82020|https://www.uniprot.org/uniprot/Q787B5|https://www.uniprot.org/uniprot/Q77SK0|https://www.uniprot.org/uniprot/Q77N36|https://www.uniprot.org/uniprot/Q76G52|https://www.uniprot.org/uniprot/Q75T09|https://www.uniprot.org/uniprot/Q6X1D5|https://www.uniprot.org/uniprot/Q6X1D1|https://www.uniprot.org/uniprot/Q6TYA0|https://www.uniprot.org/uniprot/Q6E0W7|https://www.uniprot.org/uniprot/Q66T62|https://www.uniprot.org/uniprot/Q5VKP3|https://www.uniprot.org/uniprot/Q5VKN9|https://www.uniprot.org/uniprot/Q5K2K4|https://www.uniprot.org/uniprot/Q5IX93|https://www.uniprot.org/uniprot/Q5IX92|https://www.uniprot.org/uniprot/Q5IX91|https://www.uniprot.org/uniprot/Q5IX90|https://www.uniprot.org/uniprot/Q5IX89|https://www.uniprot.org/uniprot/Q5IX88|https://www.uniprot.org/uniprot/Q5IX87|https://www.uniprot.org/uniprot/Q5GA86|https://www.uniprot.org/uniprot/Q58FH1|https://www.uniprot.org/uniprot/Q4VKV3|https://www.uniprot.org/uniprot/Q4F900|https://www.uniprot.org/uniprot/Q49LL3|https://www.uniprot.org/uniprot/Q49IU2|https://www.uniprot.org/uniprot/Q49IU1|https://www.uniprot.org/uniprot/Q49IT9|https://www.uniprot.org/uniprot/Q49IT8|https://www.uniprot.org/uniprot/Q49AV0|https://www.uniprot.org/uniprot/Q0GBY1|https://www.uniprot.org/uniprot/Q0GBX6|https://www.uniprot.org/uniprot/Q08089|https://www.uniprot.org/uniprot/P32595|https://www.uniprot.org/uniprot/P32550|https://www.uniprot.org/uniprot/P19462|https://www.uniprot.org/uniprot/P16288|https://www.uniprot.org/uniprot/P15199|https://www.uniprot.org/uniprot/P13180|https://www.uniprot.org/uniprot/P0C572|https://www.uniprot.org/uniprot/P08667|https://www.uniprot.org/uniprot/P08163|https://www.uniprot.org/uniprot/P07923|https://www.uniprot.org/uniprot/P04884|https://www.uniprot.org/uniprot/P04883|https://www.uniprot.org/uniprot/P04882|https://www.uniprot.org/uniprot/P03524|https://www.uniprot.org/uniprot/P03522|https://www.uniprot.org/uniprot/O92284|https://www.uniprot.org/uniprot/O56677|https://www.uniprot.org/uniprot/O10236|https://www.uniprot.org/uniprot/J7HBH4|https://www.uniprot.org/uniprot/D8V075|https://www.uniprot.org/uniprot/A7WNB3|https://www.uniprot.org/uniprot/A4UHQ6|https://www.uniprot.org/uniprot/A4UHQ1|https://www.uniprot.org/uniprot/A3RM22|https://www.uniprot.org/uniprot/A3F5R8|https://www.uniprot.org/uniprot/A3F5R3|https://www.uniprot.org/uniprot/A3F5Q8|https://www.uniprot.org/uniprot/A3F5N3|https://www.uniprot.org/uniprot/A3F5M3|https://www.uniprot.org/uniprot/A3F5L8
T4051 2833-2836 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T38 144-157 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sample-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 654-670 Phenotype denotes immunodeficiency http://purl.obolibrary.org/obo/HP_0002721

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T35 144-157 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T39 144-157 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T102 0-56 Sentence denotes Visualising the HIV-1 and SARS glycan shields by cryo-EM
T103 57-258 Sentence denotes HIV-1 Env is a prototypic viral class I fusion protein that exhibits extensive surface glycosylation, resulting in an effective glycan shield to aid evasion from the host adaptive immune response21,31.
T104 259-419 Sentence denotes In order to visualize the structure of the respective glycan “shields” of HIV-1 and SARS coronavirus we used single-particle cryo-electron microscopy (cryo-EM).
T105 420-574 Sentence denotes The results for HIV-1 Env were reproduced directly from Berndsen et al.51 while the previously published SARS 2P dataset52 was reprocessed for this study.
T106 575-771 Sentence denotes Although cryo-EM datasets of fully glycosylated MERS S41 and chimpanzee simian immunodeficiency virus (SIVcpz)53 are also available, only the HIV and SARS data were of sufficient quality (Fig. 5).
T107 772-947 Sentence denotes We recently showed51 that dynamics in surface exposed glycans HIV-1 Env leads to an extensive network of interactions that drive higher-order structuring in the glycan shield.
T108 948-1101 Sentence denotes This structure defines diffuse boundaries between buried and exposed surface protein surface, which can serve to define potential sites of vulnerability.
T109 1102-1282 Sentence denotes Cryo-EM captures the ensemble-average structure of biomolecules and therefore glycan dynamics results in blurred density at the resolutions necessary for building atomic structure.
T110 1283-1536 Sentence denotes However, we showed how a simple combination of low-pass filtering and auto-thresholding, as well as 3D variability analysis, can reveal the previously hidden structure of the SARS glycan shield and compare it with the HIV-1 Env glycan shield51 (Fig. 5).
T111 1537-1855 Sentence denotes We observe the nearly all-encompassing glycan density on HIV-1 Env and evidence for extensive glycan–glycan interactions, especially in the oligomannose patch regions, whereas the glycans on SARS S appear more isolated and lack the wide-ranging glycan networks that are the hallmark of an effective glycan shield54,55.
T112 1856-2307 Sentence denotes The 3D variability maps are more sensitive to low intensity signal and reveal additional glycan–glycan interactions in both maps, however the S1 receptor-binding domains in the SARS dataset were shown to exist in both up and down conformations52, leading to poor resolution and significant 2D-variability which is convolved with the variability coming from glycans and limits the interpretability of glycan shielding effects in this region of the map.
T113 2308-2383 Sentence denotes Fig. 5 Comparative cryo-EM analysis of SARS S and HIV-1 Env glycan shields.
T114 2384-2397 Sentence denotes a Left panel:
T115 2398-2606 Sentence denotes Sharpened 3.2-Å-resolution C3-symmetric cryo-EM map of SARS S 2P ectodomain52 visualized at a high contour level with disordered S1 receptor-binding and N-terminal domains extending out from the central core.
T116 2607-2620 Sentence denotes Middle panel:
T117 2621-2760 Sentence denotes Low-pass filtered (lpf) cryo-EM map of the glycoprotein visualised at a low contour level along with a simulated peptide-only map overlaid.
T118 2761-2923 Sentence denotes Right panel: SPARX 3D variability map51. b Same as in (a) but for HIV-1 Env BG505 SOSIP.664 construct in complex with three copies of RM20A3 base-specific Fabs51.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 654-670 Phenotype denotes immunodeficiency http://purl.obolibrary.org/obo/HP_0002721