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PMC:7253482 / 17585-20451 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
608 2307-2310 Gene denotes Env Gene:64006
609 2301-2306 Species denotes HIV-1 Tax:11676
610 2311-2317 Chemical denotes glycan MESH:D011134
611 2290-2294 Disease denotes SARS MESH:D045169
615 2776-2779 Gene denotes Env Gene:64006
616 2770-2775 Species denotes HIV-1 Tax:11676
617 2396-2400 Disease denotes SARS MESH:D045169
656 6-9 Gene denotes Env Gene:64006
657 385-388 Gene denotes Env Gene:64006
658 783-786 Gene denotes Env Gene:64006
659 1450-1453 Gene denotes Env Gene:64006
660 1543-1546 Gene denotes Env Gene:64006
661 0-5 Species denotes HIV-1 Tax:11676
662 276-281 Species denotes HIV-1 Tax:11676
663 286-302 Species denotes SARS coronavirus Tax:694009
664 379-384 Species denotes HIV-1 Tax:11676
665 468-474 Species denotes SARS 2 Tax:2697049
666 579-589 Species denotes chimpanzee Tax:9598
667 590-628 Species denotes simian immunodeficiency virus (SIVcpz) Tax:11723
668 777-782 Species denotes HIV-1 Tax:11676
669 1444-1449 Species denotes HIV-1 Tax:11676
670 1537-1542 Species denotes HIV-1 Tax:11676
671 128-134 Chemical denotes glycan MESH:D011134
672 256-262 Chemical denotes glycan MESH:D011134
673 769-776 Chemical denotes glycans MESH:D011134
674 876-882 Chemical denotes glycan MESH:D011134
675 1123-1129 Chemical denotes glycan MESH:D011134
676 1406-1412 Chemical denotes glycan MESH:D011134
677 1454-1460 Chemical denotes glycan MESH:D011134
678 1519-1525 Chemical denotes glycan MESH:D011134
679 1574-1580 Chemical denotes glycan MESH:D011134
680 1581-1587 Chemical denotes glycan MESH:D011134
681 1620-1632 Chemical denotes oligomannose
682 1660-1667 Chemical denotes glycans MESH:D011134
683 1725-1731 Chemical denotes glycan MESH:D011134
684 1779-1785 Chemical denotes glycan MESH:D011134
685 1888-1894 Chemical denotes glycan MESH:D011134
686 1895-1901 Chemical denotes glycan MESH:D011134
687 2156-2163 Chemical denotes glycans MESH:D011134
688 2199-2205 Chemical denotes glycan MESH:D011134
689 566-570 Disease denotes MERS MESH:D018352
690 668-672 Disease denotes SARS MESH:D045169
691 1401-1405 Disease denotes SARS MESH:D045169
692 1671-1675 Disease denotes SARS MESH:D045169
693 1976-1980 Disease denotes SARS MESH:D045169

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T100 0-3 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T101 47-54 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T102 276-279 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T103 379-382 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T104 660-663 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T105 777-780 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T106 968-975 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T107 1444-1447 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T108 1537-1540 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T109 2246-2249 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T110 2301-2304 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T111 2389-2392 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T112 2596-2599 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T113 2607-2619 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T114 2690-2693 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T115 2770-2773 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T65 286-290 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 468-472 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 597-613 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T68 668-672 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T69 1401-1405 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T70 1671-1675 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T71 1976-1980 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T72 2290-2294 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T73 2396-2400 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T103 13-14 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 579-589 http://purl.obolibrary.org/obo/NCBITaxon_9598 denotes chimpanzee
T105 614-619 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T106 1249-1250 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 1859-1865 http://purl.obolibrary.org/obo/SO_0000418 denotes signal
T108 1941-1943 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T109 2327-2328 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 2355-2356 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T111 2433-2434 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 2470-2472 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T113 2634-2635 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 2665-2666 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 2677-2684 http://purl.obolibrary.org/obo/PR_000018263 denotes peptide
T116 2745-2746 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T117 2759-2760 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T193 47-54 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T194 332-340 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T195 358-360 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T196 532-534 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T197 769-776 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T198 968-975 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T199 1050-1052 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T200 1660-1667 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T201 2156-2163 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T202 2275-2277 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T203 2386-2388 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T204 2593-2595 Chemical denotes EM http://purl.obolibrary.org/obo/CHEBI_73507
T205 2607-2619 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T206 2677-2684 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670
T207 2845-2849 Chemical denotes base http://purl.obolibrary.org/obo/CHEBI_22695

LitCovid-sample-MedDRA

Id Subject Object Predicate Lexical cue meddra_id
T6 341-351 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 166-170 http://purl.obolibrary.org/obo/IDO_0000531 denotes host
T50 597-613 http://purl.obolibrary.org/obo/IDO_0000617 denotes immunodeficiency
T51 614-619 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T52 697-704 http://purl.obolibrary.org/obo/BFO_0000019 denotes quality
T53 1021-1026 http://purl.obolibrary.org/obo/BFO_0000029 denotes sites
T54 2459-2469 http://purl.obolibrary.org/obo/OGMS_0000045 denotes disordered

LitCovid-sample-Enju

Id Subject Object Predicate Lexical cue
T8430 0-5 NN denotes HIV-1
T3174 6-9 NN denotes Env
T27555 10-12 VBZ denotes is
T55541 13-14 DT denotes a
T20248 15-25 JJ denotes prototypic
T67286 26-31 JJ denotes viral
T69498 32-37 NN denotes class
T3932 38-39 CD denotes I
T49427 40-46 NN denotes fusion
T80657 47-54 NN denotes protein
T46816 55-59 WDT denotes that
T99370 60-68 VBZ denotes exhibits
T82158 69-78 JJ denotes extensive
T40184 79-86 NN denotes surface
T83381 87-100 NN denotes glycosylation
T34922 100-101 -COMMA- denotes ,
T41135 102-111 VBG denotes resulting
T52094 112-114 IN denotes in
T41086 115-117 DT denotes an
T24478 118-127 JJ denotes effective
T12116 128-134 NN denotes glycan
T66049 135-141 NN denotes shield
T24089 142-144 TO denotes to
T80516 145-148 VB denotes aid
T40146 149-156 NN denotes evasion
T31245 157-161 IN denotes from
T10149 162-165 DT denotes the
T79574 166-170 NN denotes host
T93688 171-179 JJ denotes adaptive
T94198 180-186 JJ denotes immune
T10989 187-200 NN denotes response21,31
T32196 202-204 IN denotes In
T81817 205-210 NN denotes order
T91723 211-213 TO denotes to
T52822 214-223 VB denotes visualize
T6796 224-227 DT denotes the
T38040 228-237 NN denotes structure
T51236 238-240 IN denotes of
T17574 241-244 DT denotes the
T94895 245-255 JJ denotes respective
T2313 256-262 NN denotes glycan
T39465 263-272 NN denotes “shields”
T63649 273-275 IN denotes of
T97323 276-281 NN denotes HIV-1
T48816 282-285 CC denotes and
T59243 286-290 NN denotes SARS
T65533 291-302 NN denotes coronavirus
T26306 303-305 PRP denotes we
T89403 306-310 VBD denotes used
T31852 311-326 JJ denotes single-particle
T56676 327-340 NN denotes cryo-electron
T27050 341-351 NN denotes microscopy
T97416 352-353 -LRB- denotes (
T56321 353-360 NN denotes cryo-EM
T61586 360-361 -RRB- denotes )
T32555 363-366 DT denotes The
T47125 367-374 NNS denotes results
T36239 375-378 IN denotes for
T18889 379-384 NN denotes HIV-1
T12931 385-388 NN denotes Env
T63067 389-393 VBD denotes were
T30265 394-404 VBN denotes reproduced
T57197 405-413 RB denotes directly
T8292 414-418 IN denotes from
T31650 419-427 NNP denotes Berndsen
T37715 428-430 NNP denotes et
T19388 431-436 NN denotes al.51
T9777 437-442 IN denotes while
T55752 443-446 DT denotes the
T50993 447-457 RB denotes previously
T21233 458-467 VBN denotes published
T39264 468-472 NN denotes SARS
T63581 473-475 NN denotes 2P
T16458 476-485 NN denotes dataset52
T19972 486-489 VBD denotes was
T72393 490-501 VBN denotes reprocessed
T49131 502-505 IN denotes for
T60843 506-510 DT denotes this
T69625 511-516 NN denotes study
T12832 518-526 IN denotes Although
T24787 527-534 NN denotes cryo-EM
T29672 535-543 NNS denotes datasets
T9596 544-546 IN denotes of
T45576 547-552 RB denotes fully
T37894 553-565 VBN denotes glycosylated
T35124 566-570 NNS denotes MERS
T87593 571-574 NN denotes S41
T79382 575-578 CC denotes and
T63281 579-589 NN denotes chimpanzee
T35247 590-596 JJ denotes simian
T82138 597-613 NN denotes immunodeficiency
T35287 614-619 NN denotes virus
T14224 620-621 -LRB- denotes (
T81517 621-627 NN denotes SIVcpz
T3442 627-628 -RRB- denotes )
T14676 628-630 CD denotes 53
T32530 631-634 VBP denotes are
T45598 635-639 RB denotes also
T95444 640-649 JJ denotes available
T17171 649-650 -COMMA- denotes ,
T88916 651-655 RB denotes only
T2700 656-659 DT denotes the
T19064 660-663 NN denotes HIV
T16401 664-667 CC denotes and
T74879 668-672 NN denotes SARS
T37597 673-677 NNS denotes data
T46398 678-682 VBD denotes were
T10901 683-685 IN denotes of
T19935 686-696 JJ denotes sufficient
T58744 697-704 NN denotes quality
T47642 705-706 -LRB- denotes (
T27616 706-712 CD denotes Fig. 5
T15042 712-713 -RRB- denotes )
T64790 715-717 PRP denotes We
T12200 718-726 RB denotes recently
T55283 727-735 VBD denotes showed51
T5337 736-740 IN denotes that
T85969 741-749 NNS denotes dynamics
T15501 750-752 IN denotes in
T81842 753-760 NN denotes surface
T53947 761-768 VBN denotes exposed
T58293 769-776 NNS denotes glycans
T78469 777-782 NN denotes HIV-1
T11314 783-786 NN denotes Env
T63261 787-792 VBZ denotes leads
T50401 793-795 TO denotes to
T72222 796-798 DT denotes an
T69150 799-808 JJ denotes extensive
T26975 809-816 NN denotes network
T64977 817-819 IN denotes of
T71776 820-832 NNS denotes interactions
T7784 833-837 WDT denotes that
T35226 838-843 VBP denotes drive
T68570 844-856 JJR denotes higher-order
T34602 857-868 NN denotes structuring
T35212 869-871 IN denotes in
T61552 872-875 DT denotes the
T88226 876-882 NN denotes glycan
T2686 883-889 NN denotes shield
T70456 891-895 DT denotes This
T49009 896-905 NN denotes structure
T80667 906-913 VBZ denotes defines
T33829 914-921 JJ denotes diffuse
T1508 922-932 NNS denotes boundaries
T66208 933-940 IN denotes between
T95551 941-947 VBN denotes buried
T27513 948-951 CC denotes and
T63689 952-959 VBN denotes exposed
T23712 960-967 NN denotes surface
T90175 968-975 NN denotes protein
T66804 976-983 NN denotes surface
T71072 983-984 -COMMA- denotes ,
T80348 985-990 WDT denotes which
T9316 991-994 MD denotes can
T90504 995-1000 VB denotes serve
T42110 1001-1003 TO denotes to
T69932 1004-1010 VB denotes define
T67682 1011-1020 JJ denotes potential
T2204 1021-1026 NNS denotes sites
T70578 1027-1029 IN denotes of
T95274 1030-1043 NN denotes vulnerability
T46703 1045-1052 NN denotes Cryo-EM
T30395 1053-1061 VBZ denotes captures
T87072 1062-1065 DT denotes the
T44958 1066-1082 JJ denotes ensemble-average
T7879 1083-1092 NN denotes structure
T75651 1093-1095 IN denotes of
T66273 1096-1108 NNS denotes biomolecules
T73691 1109-1112 CC denotes and
T31109 1113-1122 RB denotes therefore
T12255 1123-1129 NN denotes glycan
T11220 1130-1138 NNS denotes dynamics
T43250 1139-1146 VBZ denotes results
T52169 1147-1149 IN denotes in
T64021 1150-1157 VBN denotes blurred
T49153 1158-1165 NN denotes density
T2441 1166-1168 IN denotes at
T80700 1169-1172 DT denotes the
T16085 1173-1184 NNS denotes resolutions
T86172 1185-1194 JJ denotes necessary
T28589 1195-1198 IN denotes for
T42839 1199-1207 VBG denotes building
T3599 1208-1214 JJ denotes atomic
T43748 1215-1224 NN denotes structure
T10071 1226-1233 RB denotes However
T88433 1233-1234 -COMMA- denotes ,
T97506 1235-1237 PRP denotes we
T94206 1238-1244 VBD denotes showed
T91691 1245-1248 WRB denotes how
T17411 1249-1250 DT denotes a
T2527 1251-1257 JJ denotes simple
T82430 1258-1269 NN denotes combination
T32469 1270-1272 IN denotes of
T40028 1273-1281 JJ denotes low-pass
T93291 1282-1291 NN denotes filtering
T10413 1292-1295 CC denotes and
T2487 1296-1313 NN denotes auto-thresholding
T78379 1313-1314 -COMMA- denotes ,
T27010 1315-1317 RB denotes as
T32044 1318-1322 RB denotes well
T89162 1323-1325 IN denotes as
T8187 1326-1328 NN denotes 3D
T99213 1329-1340 NN denotes variability
T14190 1341-1349 NN denotes analysis
T81037 1349-1350 -COMMA- denotes ,
T87732 1351-1354 MD denotes can
T9264 1355-1361 VB denotes reveal
T36472 1362-1365 DT denotes the
T15866 1366-1376 RB denotes previously
T33845 1377-1383 VBN denotes hidden
T31709 1384-1393 NN denotes structure
T97881 1394-1396 IN denotes of
T77189 1397-1400 DT denotes the
T22984 1401-1405 NNP denotes SARS
T32877 1406-1412 NN denotes glycan
T15037 1413-1419 NN denotes shield
T70541 1420-1423 CC denotes and
T30415 1424-1431 VB denotes compare
T37461 1432-1434 PRP denotes it
T52236 1435-1439 IN denotes with
T25513 1440-1443 DT denotes the
T63380 1444-1449 NN denotes HIV-1
T80636 1450-1453 NN denotes Env
T69159 1454-1460 NN denotes glycan
T3337 1461-1469 NN denotes shield51
T64033 1470-1471 -LRB- denotes (
T94502 1471-1477 CD denotes Fig. 5
T94581 1477-1478 -RRB- denotes )
T60289 1480-1482 PRP denotes We
T75223 1483-1490 VBP denotes observe
T57545 1491-1494 DT denotes the
T48330 1495-1501 RB denotes nearly
T87308 1502-1518 JJ denotes all-encompassing
T1558 1519-1525 NN denotes glycan
T99824 1526-1533 NN denotes density
T59798 1534-1536 IN denotes on
T56235 1537-1542 NN denotes HIV-1
T14383 1543-1546 NN denotes Env
T33263 1547-1550 CC denotes and
T4213 1551-1559 NN denotes evidence
T91161 1560-1563 IN denotes for
T79082 1564-1573 JJ denotes extensive
T66189 1574-1587 NN denotes glycan–glycan
T48593 1588-1600 NNS denotes interactions
T42535 1600-1601 -COMMA- denotes ,
T14663 1602-1612 RB denotes especially
T44869 1613-1615 IN denotes in
T77065 1616-1619 DT denotes the
T90752 1620-1632 NN denotes oligomannose
T24864 1633-1638 NN denotes patch
T20998 1639-1646 NNS denotes regions
T55492 1646-1647 -COMMA- denotes ,
T69929 1648-1655 IN denotes whereas
T90575 1656-1659 DT denotes the
T59031 1660-1667 NNS denotes glycans
T94235 1668-1670 IN denotes on
T22232 1671-1675 NNP denotes SARS
T7541 1676-1677 NNP denotes S
T66013 1678-1684 VBP denotes appear
T27090 1685-1689 RBR denotes more
T7370 1690-1698 VBN denotes isolated
T67487 1699-1702 CC denotes and
T50530 1703-1707 VBP denotes lack
T21892 1708-1711 DT denotes the
T55852 1712-1724 JJ denotes wide-ranging
T70160 1725-1731 NN denotes glycan
T80844 1732-1740 NNS denotes networks
T83936 1741-1745 WDT denotes that
T81018 1746-1749 VBP denotes are
T68036 1750-1753 DT denotes the
T82951 1754-1762 NN denotes hallmark
T16903 1763-1765 IN denotes of
T2902 1766-1768 DT denotes an
T18742 1769-1778 JJ denotes effective
T88640 1779-1785 NN denotes glycan
T57983 1786-1797 NN denotes shield54,55
T96638 1799-1802 DT denotes The
T9355 1803-1805 NN denotes 3D
T47791 1806-1817 NN denotes variability
T79677 1818-1822 NNS denotes maps
T51290 1823-1826 VBP denotes are
T66740 1827-1831 RBR denotes more
T28675 1832-1841 JJ denotes sensitive
T51626 1842-1844 TO denotes to
T96563 1845-1848 JJ denotes low
T5756 1849-1858 NN denotes intensity
T42122 1859-1865 NN denotes signal
T93380 1866-1869 CC denotes and
T52275 1870-1876 VBP denotes reveal
T65761 1877-1887 JJ denotes additional
T40659 1888-1901 NN denotes glycan–glycan
T18648 1902-1914 NNS denotes interactions
T53697 1915-1917 IN denotes in
T13379 1918-1922 DT denotes both
T61777 1923-1927 NNS denotes maps
T1991 1927-1928 -COMMA- denotes ,
T10706 1929-1936 RB denotes however
T21547 1937-1940 DT denotes the
T89902 1941-1943 NN denotes S1
T24397 1944-1960 JJ denotes receptor-binding
T67026 1961-1968 NNS denotes domains
T98351 1969-1971 IN denotes in
T69700 1972-1975 DT denotes the
T97210 1976-1980 NN denotes SARS
T19203 1981-1988 NN denotes dataset
T21495 1989-1993 VBD denotes were
T3893 1994-1999 VBN denotes shown
T33461 2000-2002 TO denotes to
T68704 2003-2008 VB denotes exist
T1970 2009-2011 IN denotes in
T91066 2012-2016 CC denotes both
T75781 2017-2019 RB denotes up
T44006 2020-2023 CC denotes and
T47879 2024-2028 IN denotes down
T22009 2029-2044 NN denotes conformations52
T80149 2044-2045 -COMMA- denotes ,
T10724 2046-2053 VBG denotes leading
T29355 2054-2056 TO denotes to
T48291 2057-2061 JJ denotes poor
T15651 2062-2072 NN denotes resolution
T15044 2073-2076 CC denotes and
T36313 2077-2088 JJ denotes significant
T78120 2089-2103 NN denotes 2D-variability
T97054 2104-2109 WDT denotes which
T80897 2110-2112 VBZ denotes is
T73857 2113-2122 VBN denotes convolved
T52453 2123-2127 IN denotes with
T12417 2128-2131 DT denotes the
T9415 2132-2143 NN denotes variability
T91463 2144-2150 VBG denotes coming
T37758 2151-2155 IN denotes from
T69399 2156-2163 NNS denotes glycans
T37469 2164-2167 CC denotes and
T7534 2168-2174 VBZ denotes limits
T29335 2175-2178 DT denotes the
T16169 2179-2195 NN denotes interpretability
T54909 2196-2198 IN denotes of
T36751 2199-2205 NN denotes glycan
T68517 2206-2215 NN denotes shielding
T73688 2216-2223 NNS denotes effects
T27520 2224-2226 IN denotes in
T1634 2227-2231 DT denotes this
T15004 2232-2238 NN denotes region
T14842 2239-2241 IN denotes of
T18381 2242-2245 DT denotes the
T85741 2246-2249 NN denotes map
T77710 2251-2255 NNP denotes Fig.
T43639 2256-2257 CD denotes 5
T80136 2258-2269 JJ denotes Comparative
T57723 2270-2277 NN denotes cryo-EM
T19047 2278-2286 NN denotes analysis
T52944 2287-2289 IN denotes of
T86979 2290-2294 NNP denotes SARS
T71022 2295-2296 NNP denotes S
T87387 2297-2300 CC denotes and
T92374 2301-2306 NN denotes HIV-1
T58960 2307-2310 NN denotes Env
T67673 2311-2317 NN denotes glycan
T21302 2318-2325 NNS denotes shields
T48820 2327-2328 DT denotes a
T79466 2329-2333 NNP denotes Left
T16113 2334-2339 NN denotes panel
T98169 2339-2340 -COLON- denotes :
T63629 2341-2350 VBN denotes Sharpened
T90429 2351-2367 JJ denotes 3.2-Å-resolution
T6423 2368-2380 JJ denotes C3-symmetric
T13124 2381-2388 NN denotes cryo-EM
T56273 2389-2392 NN denotes map
T86558 2393-2395 IN denotes of
T37174 2396-2400 NNP denotes SARS
T84496 2401-2402 NNP denotes S
T86959 2403-2405 NN denotes 2P
T75209 2406-2418 NN denotes ectodomain52
T37067 2419-2429 VBN denotes visualized
T22530 2430-2432 IN denotes at
T60171 2433-2434 DT denotes a
T27128 2435-2439 JJ denotes high
T94740 2440-2447 NN denotes contour
T58510 2448-2453 NN denotes level
T66412 2454-2458 IN denotes with
T32176 2459-2469 VBN denotes disordered
T5395 2470-2472 NN denotes S1
T34000 2473-2489 JJ denotes receptor-binding
T54890 2490-2493 CC denotes and
T9018 2494-2504 JJ denotes N-terminal
T68442 2505-2512 NNS denotes domains
T72184 2513-2522 VBG denotes extending
T12801 2523-2526 RP denotes out
T26493 2527-2531 IN denotes from
T4854 2532-2535 DT denotes the
T35333 2536-2543 JJ denotes central
T39891 2544-2548 NN denotes core
T4786 2550-2556 JJ denotes Middle
T40721 2557-2562 NN denotes panel
T2753 2562-2563 -COLON- denotes :
T68941 2564-2572 JJ denotes Low-pass
T98545 2573-2581 VBN denotes filtered
T5712 2582-2583 -LRB- denotes (
T65635 2583-2586 NN denotes lpf
T36825 2586-2587 -RRB- denotes )
T66628 2588-2595 NN denotes cryo-EM
T90188 2596-2599 NN denotes map
T57750 2600-2602 IN denotes of
T25808 2603-2606 DT denotes the
T69826 2607-2619 NN denotes glycoprotein
T87240 2620-2630 VBN denotes visualised
T62278 2631-2633 IN denotes at
T88612 2634-2635 DT denotes a
T55069 2636-2639 JJ denotes low
T38898 2640-2647 NN denotes contour
T68027 2648-2653 NN denotes level
T69920 2654-2659 IN denotes along
T22579 2660-2664 IN denotes with
T51416 2665-2666 DT denotes a
T26917 2667-2676 JJ denotes simulated
T72481 2677-2689 JJ denotes peptide-only
T91266 2690-2693 NN denotes map
T43073 2694-2702 NN denotes overlaid
T20774 2704-2709 JJ denotes Right
T74921 2710-2715 NN denotes panel
T5294 2715-2716 -COLON- denotes :
T27512 2717-2722 NN denotes SPARX
T17578 2723-2725 NN denotes 3D
T69974 2726-2737 NN denotes variability
T86316 2738-2744 NN denotes map51.
T39562 2745-2746 NN denotes b
T43304 2747-2751 JJ denotes Same
T52255 2752-2754 IN denotes as
T48004 2755-2757 IN denotes in
T51718 2758-2759 -LRB- denotes (
T36617 2759-2760 DT denotes a
T97382 2760-2761 -RRB- denotes )
T54597 2762-2765 CC denotes but
T81241 2766-2769 IN denotes for
T90782 2770-2775 NN denotes HIV-1
T13950 2776-2779 NNP denotes Env
T55209 2780-2785 NN denotes BG505
T53941 2786-2795 NN denotes SOSIP.664
T83312 2796-2805 NN denotes construct
T96415 2806-2808 IN denotes in
T45843 2809-2816 NN denotes complex
T56194 2817-2821 IN denotes with
T46276 2822-2827 CD denotes three
T95298 2828-2834 NNS denotes copies
T19490 2835-2837 IN denotes of
T71992 2838-2844 NN denotes RM20A3
T28802 2845-2858 JJ denotes base-specific
T65942 2859-2865 NN denotes Fabs51
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
T99 0-3 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T100 47-54 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T101 276-279 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T102 379-382 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T103 660-663 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T104 777-780 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T105 968-975 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T106 1444-1447 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T107 1537-1540 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T108 2246-2249 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T109 2301-2304 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T110 2389-2392 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T111 2596-2599 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T112 2607-2619 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T113 2690-2693 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T114 2770-2773 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T135 47-54 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T136 769-776 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T137 968-975 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T138 1660-1667 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T139 2156-2163 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T140 2607-2619 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T141 2677-2684 Chemical denotes peptide http://purl.obolibrary.org/obo/CHEBI_16670

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T124 0-5 Species denotes HIV-1 NCBItxid:11676
T125 276-281 Species denotes HIV-1 NCBItxid:11676
T126 286-302 Species denotes SARS coronavirus NCBItxid:694009
T127 286-290 Species denotes SARS NCBItxid:694009
T128 379-384 Species denotes HIV-1 NCBItxid:11676
T129 468-472 Species denotes SARS NCBItxid:694009
T130 566-570 Species denotes MERS NCBItxid:1335626
T131 579-589 Species denotes chimpanzee NCBItxid:9598
T132 590-619 Species denotes simian immunodeficiency virus NCBItxid:11723
T133 621-627 Species denotes SIVcpz NCBItxid:388909
T134 660-663 Species denotes HIV NCBItxid:57667|NCBItxid:35274|NCBItxid:12721|NCBItxid:11709|NCBItxid:11676
T139 668-672 Species denotes SARS NCBItxid:694009
T140 777-782 Species denotes HIV-1 NCBItxid:11676
T141 1401-1405 Species denotes SARS NCBItxid:694009
T142 1444-1449 Species denotes HIV-1 NCBItxid:11676
T143 1537-1542 Species denotes HIV-1 NCBItxid:11676
T144 1671-1675 Species denotes SARS NCBItxid:694009
T145 1976-1980 Species denotes SARS NCBItxid:694009
T146 2290-2294 Species denotes SARS NCBItxid:694009
T147 2301-2306 Species denotes HIV-1 NCBItxid:11676
T148 2396-2400 Species denotes SARS NCBItxid:694009
T149 2770-2775 Species denotes HIV-1 NCBItxid:11676

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T103 0-201 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 202-362 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 363-517 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 518-714 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 715-890 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 891-1044 Sentence denotes This structure defines diffuse boundaries between buried and exposed surface protein surface, which can serve to define potential sites of vulnerability.
T109 1045-1225 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 1226-1479 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 1480-1798 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 1799-2250 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 2251-2326 Sentence denotes Fig. 5 Comparative cryo-EM analysis of SARS S and HIV-1 Env glycan shields.
T114 2327-2340 Sentence denotes a Left panel:
T115 2341-2549 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 2550-2563 Sentence denotes Middle panel:
T117 2564-2703 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 2704-2866 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
T60 286-290 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T61 468-472 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T62 597-613 Disease denotes immunodeficiency http://purl.obolibrary.org/obo/MONDO_0021094
T63 668-672 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T64 1401-1405 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T65 1671-1675 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 1976-1980 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 2290-2294 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T68 2396-2400 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-sample-Pubtator

Id Subject Object Predicate Lexical cue pubann:denotes
661 0-5 Species denotes HIV-1 Tax:11676
656 6-9 Gene denotes Env Gene:64006
671 128-134 Chemical denotes glycan MESH:D011134
672 256-262 Chemical denotes glycan MESH:D011134
662 276-281 Species denotes HIV-1 Tax:11676
663 286-302 Species denotes SARS coronavirus Tax:694009
664 379-384 Species denotes HIV-1 Tax:11676
657 385-388 Gene denotes Env Gene:64006
665 468-474 Species denotes SARS 2 Tax:2697049
689 566-570 Disease denotes MERS MESH:D018352
666 579-589 Species denotes chimpanzee Tax:9598
667 590-628 Species denotes simian immunodeficiency virus (SIVcpz) Tax:11723
690 668-672 Disease denotes SARS MESH:D045169
673 769-776 Chemical denotes glycans MESH:D011134
668 777-782 Species denotes HIV-1 Tax:11676
658 783-786 Gene denotes Env Gene:64006
674 876-882 Chemical denotes glycan MESH:D011134
675 1123-1129 Chemical denotes glycan MESH:D011134
691 1401-1405 Disease denotes SARS MESH:D045169
676 1406-1412 Chemical denotes glycan MESH:D011134
669 1444-1449 Species denotes HIV-1 Tax:11676
659 1450-1453 Gene denotes Env Gene:64006
677 1454-1460 Chemical denotes glycan MESH:D011134
678 1519-1525 Chemical denotes glycan MESH:D011134
670 1537-1542 Species denotes HIV-1 Tax:11676
660 1543-1546 Gene denotes Env Gene:64006
679 1574-1580 Chemical denotes glycan MESH:D011134
680 1581-1587 Chemical denotes glycan MESH:D011134
681 1620-1632 Chemical denotes oligomannose
682 1660-1667 Chemical denotes glycans MESH:D011134
692 1671-1675 Disease denotes SARS MESH:D045169
683 1725-1731 Chemical denotes glycan MESH:D011134
684 1779-1785 Chemical denotes glycan MESH:D011134
685 1888-1894 Chemical denotes glycan MESH:D011134
686 1895-1901 Chemical denotes glycan MESH:D011134
693 1976-1980 Disease denotes SARS MESH:D045169
687 2156-2163 Chemical denotes glycans MESH:D011134
688 2199-2205 Chemical denotes glycan MESH:D011134
611 2290-2294 Disease denotes SARS MESH:D045169
609 2301-2306 Species denotes HIV-1 Tax:11676
608 2307-2310 Gene denotes Env Gene:64006
610 2311-2317 Chemical denotes glycan MESH:D011134
617 2396-2400 Disease denotes SARS MESH:D045169
616 2770-2775 Species denotes HIV-1 Tax:11676
615 2776-2779 Gene denotes Env Gene:64006

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T3769 6-9 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3771 385-388 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3773 783-786 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3775 960-975 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 1450-1453 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3962 1543-1546 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3964 2307-2310 Protein denotes Env https://www.uniprot.org/uniprot/C1JJY3|https://www.uniprot.org/uniprot/P24123
T3966 2607-2619 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 2776-2779 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 87-100 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sample-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 597-613 Phenotype denotes immunodeficiency http://purl.obolibrary.org/obo/HP_0002721

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T35 87-100 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T39 87-100 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T103 0-201 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 202-362 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 363-517 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 518-714 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 715-890 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 891-1044 Sentence denotes This structure defines diffuse boundaries between buried and exposed surface protein surface, which can serve to define potential sites of vulnerability.
T109 1045-1225 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 1226-1479 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 1480-1798 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 1799-2250 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 2251-2326 Sentence denotes Fig. 5 Comparative cryo-EM analysis of SARS S and HIV-1 Env glycan shields.
T114 2327-2340 Sentence denotes a Left panel:
T115 2341-2549 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 2550-2563 Sentence denotes Middle panel:
T117 2564-2703 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 2704-2866 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 597-613 Phenotype denotes immunodeficiency http://purl.obolibrary.org/obo/HP_0002721