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PMC:7128678 / 14486-17074 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
450 50-51 Gene denotes S Gene:43740568
451 39-49 Species denotes SARS-CoV-2 Tax:2697049
459 849-850 Gene denotes S Gene:43740568
460 778-779 Gene denotes S Gene:43740568
461 674-675 Gene denotes S Gene:43740568
462 565-566 Gene denotes S Gene:43740568
463 506-516 Species denotes SARS-CoV-2 Tax:2697049
464 517-522 Gene denotes spike Gene:43740568
465 1137-1148 Chemical denotes ganglioside MESH:D005732
472 343-344 Gene denotes S Gene:43740568
473 275-276 Gene denotes S Gene:43740568
474 109-119 Species denotes SARS-CoV-2 Tax:2697049
475 264-274 Species denotes SARS-CoV-2 Tax:2697049
476 156-168 Chemical denotes gangliosides MESH:D005732
477 228-234 Chemical denotes CLQ-OH
481 1308-1319 Chemical denotes ganglioside MESH:D005732
482 1588-1599 Chemical denotes ganglioside MESH:D005732
483 1644-1649 Chemical denotes lipid MESH:D008055
494 1787-1798 Chemical denotes ganglioside MESH:D005732
495 2029-2032 Chemical denotes Gly MESH:D005998
496 2034-2037 Chemical denotes Pro MESH:D011392
497 2045-2048 Chemical denotes Ser MESH:D012694
498 2145-2156 Chemical denotes ganglioside MESH:D005732
499 2388-2391 Chemical denotes Gly MESH:D005998
500 2393-2396 Chemical denotes Pro MESH:D011392
501 2404-2407 Chemical denotes Ser MESH:D012694
502 2441-2452 Chemical denotes ganglioside MESH:D005732
503 2555-2566 Chemical denotes ganglioside MESH:D005732

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T320 39-49 SP_7 denotes SARS-CoV-2
T321 50-59 PG_1 denotes S protein
T322 109-119 SP_7 denotes SARS-CoV-2
T323 140-155 GO:0005886 denotes plasma membrane
T324 156-168 CHEBI:5386;CHEBI:5386 denotes gangliosides
T325 264-274 SP_7 denotes SARS-CoV-2
T326 275-284 PG_1 denotes S protein
T327 384-391 SO:0000417 denotes domains
T328 409-414 NCBITaxon:10239;GO:0019031 denotes viral
T329 415-423 GO:0019031 denotes envelope
T330 438-452 SO:0000409 denotes binding region
T331 506-516 SP_7 denotes SARS-CoV-2
T332 565-574 PG_1 denotes S protein
T333 674-683 PG_1 denotes S protein
T334 699-706 SO:0001117 denotes α-helix
T335 778-787 PG_1 denotes S protein
T336 849-858 PG_1 denotes S protein
T337 887-893 SO:0000417 denotes domain
T338 914-923 PG_1 denotes S protein
T339 1137-1148 CHEBI:28892;CHEBI:28892 denotes ganglioside
T340 1157-1163 SO:0000417 denotes domain
T352 1244-1249 G_3;PG_10;PR:000003622 denotes ACE-2
T353 1308-1319 CHEBI:16856;CHEBI:16856 denotes ganglioside
T354 1363-1369 SO:0000417 denotes domain
T355 1377-1378 PG_18 denotes S
T356 1379-1391 PG_18;CHEBI:17089;CHEBI:17089;BV_11 denotes glycoprotein
T357 1588-1599 CHEBI:5386;CHEBI:5386 denotes ganglioside
T358 1605-1620 GO:0005886 denotes plasma membrane
T359 1621-1632 GO:0098857 denotes microdomain
T360 1644-1649 CHEBI:18059;CHEBI:18059;GO:0045121 denotes lipid
T361 1650-1654 GO:0045121 denotes raft
T362 1777-1786 SO:0000993 denotes consensus
T363 1787-1798 CHEBI:16856;CHEBI:16856 denotes ganglioside
T364 1807-1814 SO:0000417 denotes domains
T365 2145-2156 CHEBI:28892;CHEBI:28892 denotes ganglioside
T366 2165-2171 SO:0000417 denotes domain
T367 2441-2452 CHEBI:28892;CHEBI:28892 denotes ganglioside
T368 2555-2566 CHEBI:28892;CHEBI:28892 denotes ganglioside

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T65 52-59 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T66 140-155 Body_part denotes plasma membrane http://purl.org/sig/ont/fma/fma63841
T67 156-168 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T68 277-284 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T69 345-353 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T70 527-534 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T71 567-574 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T72 676-683 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T73 701-706 Body_part denotes helix http://purl.org/sig/ont/fma/fma60992
T74 780-787 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T75 851-858 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T76 916-923 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T77 1073-1083 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T78 1137-1148 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T79 1308-1319 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T80 1347-1351 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T81 1379-1391 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T82 1443-1453 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T83 1588-1599 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T84 1605-1620 Body_part denotes plasma membrane http://purl.org/sig/ont/fma/fma63841
T85 1644-1649 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T86 1660-1670 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T87 1787-1798 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T88 1874-1884 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T89 2007-2017 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T90 2145-2156 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T91 2355-2365 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T92 2441-2452 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T93 2555-2566 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T7 701-706 Body_part denotes helix http://purl.obolibrary.org/obo/UBERON_0002488
T8 746-763 Body_part denotes Surface structure http://purl.obolibrary.org/obo/UBERON_0003102
T9 1468-1471 Body_part denotes tip http://purl.obolibrary.org/obo/UBERON_2001840
T10 1729-1732 Body_part denotes tip http://purl.obolibrary.org/obo/UBERON_2001840
T11 2518-2521 Body_part denotes tip http://purl.obolibrary.org/obo/UBERON_2001840

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T27 32-35 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T29 39-47 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 109-117 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 264-272 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 467-470 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T34 506-514 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 895-898 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T37 960-963 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T39 1100-1103 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T41 1402-1405 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T43 1412-1415 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T45 1479-1482 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T47 1740-1743 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T49 2194-2197 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T51 2529-2532 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T95 140-146 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T96 147-155 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T97 310-311 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T98 331-332 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T99 537-538 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T100 575-578 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T101 579-580 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T102 639-640 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T103 950-951 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 1073-1092 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T105 1073-1092 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T106 1125-1126 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 1347-1351 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T108 1443-1462 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T109 1443-1462 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T110 1526-1527 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 1586-1587 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 1605-1611 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T113 1612-1620 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T114 1642-1643 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T115 1853-1854 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 1874-1893 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T117 1874-1893 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T118 2547-2548 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T277 52-59 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T278 156-168 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T279 277-284 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T280 345-353 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T281 527-534 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T282 567-574 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T283 676-683 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T284 780-787 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T285 851-858 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T286 916-923 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T287 1073-1083 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T288 1073-1078 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T289 1079-1083 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T290 1137-1148 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T291 1308-1319 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T292 1379-1391 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T293 1443-1453 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T294 1443-1448 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T295 1449-1453 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T296 1588-1599 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T297 1644-1649 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T298 1660-1670 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T299 1660-1665 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T300 1666-1670 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T301 1787-1798 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T302 1874-1884 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T303 1874-1879 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T304 1880-1884 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T305 2007-2017 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T306 2007-2012 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T307 2013-2017 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T308 2029-2032 Chemical denotes Gly http://purl.obolibrary.org/obo/CHEBI_15428
T309 2034-2037 Chemical denotes Pro http://purl.obolibrary.org/obo/CHEBI_50342
T310 2045-2048 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T312 2070-2081 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232
T313 2145-2156 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T314 2355-2365 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T315 2355-2360 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T316 2361-2365 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T317 2388-2391 Chemical denotes Gly http://purl.obolibrary.org/obo/CHEBI_15428
T318 2393-2396 Chemical denotes Pro http://purl.obolibrary.org/obo/CHEBI_50342
T319 2404-2407 Chemical denotes Ser http://purl.obolibrary.org/obo/CHEBI_17115|http://purl.obolibrary.org/obo/CHEBI_29999
T321 2441-2452 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T322 2555-2566 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T105 0-59 Sentence denotes 3.4 Structural analysis of the NTD of SARS-CoV-2 S protein
T106 60-235 Sentence denotes The next step of this study was to determine how SARS-CoV-2 could interact with plasma membrane gangliosides, and whether such interaction could be affected by CLQ and CLQ-OH.
T107 236-315 Sentence denotes The global structure of the SARS-CoV-2 S protein [16] is shown in Fig. 5 (a–d).
T108 316-471 Sentence denotes It consists of a trimer of S proteins, each harbouring two distinct domains distant from the viral envelope: the receptor-binding region (RBD) and the NTD.
T109 472-1164 Sentence denotes Fig. 5 Structural features of the SARS-CoV-2 spike (S) protein. (a) Trimeric structure (each S protein has a distinct surface colour, ‘blue’, ‘yellow’ and ‘purple’). (b) Ribbon representation of ‘blue’ S protein in the trimer (α-helix, red; β-strand, blue; coil, grey). (c) Surface structure of the ‘blue’ S protein isolated from the trimer. (d) Ribbon structure of the ‘blue’ S protein. (e) Zoom on the N-terminal domain (NTD) of the ‘blue’ S protein. (f,g) Molecular model of a minimal NTD obtained with Hyperchem [ribbon in representation in (f), surface rendering in (g)]. (h) Highlighting of the amino acid residues of the NTD that could belong to a potential ganglioside-binding domain.
T110 1165-1407 Sentence denotes It was reasoned that if the RBD is engaged in functional interactions with the ACE-2 receptor, it would be interesting to search for potential ganglioside-binding sites on the other cell-accessible domain of the S glycoprotein (i.e. the NTD).
T111 1408-1463 Sentence denotes The NTD contains approximately 290 amino acid residues.
T112 1464-1655 Sentence denotes The tip of the NTD was of particular interest, as it displays a flat interface Fig. 5(f) ideally positioned for targeting a ganglioside-rich plasma membrane microdomain, such as a lipid raft.
T113 1656-1820 Sentence denotes The amino acid sequence of the planar interfacial surface located at the tip of the NTD was analysed for the presence of consensus ganglioside-binding domains [20].
T114 1821-1928 Sentence denotes These motifs are constituted by a triad of mandatory amino acid residues such as (K,R)-Xn-(F,Y,W)-Xn-(K,R).
T115 1929-2058 Sentence denotes The Xn intercalating segments, usually four to five residues, may contain any amino acid, but often Gly, Pro and/or Ser residues.
T116 2059-2198 Sentence denotes The strict application of this algorithm did not allow the detection of any potential ganglioside-binding domain in this region of the NTD.
T117 2199-2306 Sentence denotes However, an intriguing over-representation of aromatic and basic residues was found in the 129–158 segment:
T118 2307-2346 Sentence denotes 129-KVCEFQFCNDPFLGVYYHKNNKSWMESEFR-158.
T119 2347-2468 Sentence denotes This 30-amino acid stretch also contains Gly, Pro and/or Ser residues that are often found in ganglioside-binding motifs.
T120 2469-2588 Sentence denotes These observations supported the notion that the tip of the NTD could display a large ganglioside-attachment interface.

2_test

Id Subject Object Predicate Lexical cue
32251731-32075877-48149953 286-288 32075877 denotes 16
T65765 286-288 32075877 denotes 16