> top > docs > PMC:7219429 > spans > 17801-20735 > annotations

PMC:7219429 / 17801-20735 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T102 67-78 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T103 85-92 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T104 151-163 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T105 334-346 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T106 511-518 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T107 578-588 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T108 611-618 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T109 720-725 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T110 828-840 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T111 862-873 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T112 1691-1698 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T113 1716-1721 Body_part denotes lipid http://purl.org/sig/ont/fma/fma67264
T114 1743-1755 Body_part denotes gangliosides http://purl.org/sig/ont/fma/fma82816
T115 2029-2036 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T116 2045-2055 Body_part denotes Amino acid http://purl.org/sig/ont/fma/fma82739
T117 2083-2094 Body_part denotes ganglioside http://purl.org/sig/ont/fma/fma82816
T118 2138-2145 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T119 2478-2488 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T120 2708-2713 Body_part denotes colon http://purl.org/sig/ont/fma/fma14543

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T13 2708-2713 Body_part denotes colon http://purl.obolibrary.org/obo/UBERON_0001155

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T62 494-502 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T63 811-814 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T65 1067-1075 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T66 1255-1263 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T67 1335-1338 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T69 1374-1382 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T70 1494-1498 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T71 1604-1612 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T72 2012-2015 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T74 2121-2129 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T75 2194-2202 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T76 2430-2438 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T77 2802-2805 Disease denotes PAM http://purl.obolibrary.org/obo/MONDO_0018959
T78 2918-2921 Disease denotes PAM http://purl.obolibrary.org/obo/MONDO_0018959

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T179 112-114 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T180 467-468 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 578-597 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T182 578-597 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T183 750-752 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T184 853-854 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T185 1157-1160 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T186 1231-1234 http://purl.obolibrary.org/obo/NCBITaxon_9397 denotes bat
T187 1424-1427 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T188 1428-1429 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T189 1468-1474 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T190 1480-1485 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T191 1534-1535 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T192 1635-1640 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T193 1663-1665 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T194 1714-1715 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T195 1856-1858 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T196 1982-1983 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T197 2306-2309 http://purl.obolibrary.org/obo/CLO_0001002 denotes 162
T198 2391-2396 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T199 2401-2407 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes animal
T200 2408-2415 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T201 2706-2707 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T202 2708-2713 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colon
T203 2823-2824 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T313 67-78 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T314 85-92 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T315 112-114 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T316 147-150 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T319 151-163 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T320 191-197 Chemical denotes lipids http://purl.obolibrary.org/obo/CHEBI_18059
T321 204-217 Chemical denotes sphingomyelin http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583
T323 222-233 Chemical denotes cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T324 334-346 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T325 361-372 Chemical denotes cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T326 377-390 Chemical denotes sphingomyelin http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583
T328 440-443 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T331 511-518 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T332 578-588 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T333 578-583 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T334 584-588 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T335 611-618 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T336 640-643 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T337 701-704 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T340 720-725 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T341 828-840 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T342 862-873 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T343 874-877 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T344 1663-1665 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T345 1681-1684 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T348 1691-1698 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T349 1716-1721 Chemical denotes lipid http://purl.obolibrary.org/obo/CHEBI_18059
T350 1739-1742 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T353 1743-1755 Chemical denotes gangliosides http://purl.obolibrary.org/obo/CHEBI_28892
T354 1779-1790 Chemical denotes cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T355 1792-1796 Chemical denotes chol http://purl.obolibrary.org/obo/CHEBI_16113
T356 1806-1819 Chemical denotes sphingomyelin http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583
T358 1821-1823 Chemical denotes SM http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_74817|http://purl.obolibrary.org/obo/CHEBI_17636
T361 1825-1831 Chemical denotes lipids http://purl.obolibrary.org/obo/CHEBI_18059
T362 1856-1858 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T363 1942-1953 Chemical denotes Cholesterol http://purl.obolibrary.org/obo/CHEBI_16113
T364 1958-1971 Chemical denotes sphingomyelin http://purl.obolibrary.org/obo/CHEBI_17636|http://purl.obolibrary.org/obo/CHEBI_64583
T366 1993-1996 Chemical denotes GM1 http://purl.obolibrary.org/obo/CHEBI_18216|http://purl.obolibrary.org/obo/CHEBI_61048|http://purl.obolibrary.org/obo/CHEBI_73110
T369 2029-2036 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T370 2045-2055 Chemical denotes Amino acid http://purl.obolibrary.org/obo/CHEBI_33704
T371 2051-2055 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T372 2083-2094 Chemical denotes ganglioside http://purl.obolibrary.org/obo/CHEBI_28892
T373 2095-2098 Chemical denotes ATM http://purl.obolibrary.org/obo/CHEBI_2955
T374 2138-2145 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T375 2157-2162 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T376 2363-2368 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T377 2478-2488 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T378 2478-2483 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T379 2484-2488 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T380 2802-2805 Chemical denotes PAM http://purl.obolibrary.org/obo/CHEBI_51135|http://purl.obolibrary.org/obo/CHEBI_60882
T382 2918-2921 Chemical denotes PAM http://purl.obolibrary.org/obo/CHEBI_51135|http://purl.obolibrary.org/obo/CHEBI_60882

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T18 147-150 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T19 440-443 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T20 701-704 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T21 1681-1684 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T22 1739-1742 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050
T23 1993-1996 GlycoEpitope denotes GM1 http://www.glycoepitope.jp/epitopes/EP0050

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T133 0-240 Sentence denotes Based on recent in-silico data that led to the characterization of ganglioside-spike protein interactions [10], MD simulations were performed with GM1 gangliosides surrounded by typical raft lipids, i.e. sphingomyelin and cholesterol (Figs.
T134 241-251 Sentence denotes 5 and 6 ).
T135 252-352 Sentence denotes These new data confirmed and extended our previous results obtained with isolated gangliosides [10].
T136 353-528 Sentence denotes Indeed, cholesterol and sphingomyelin appeared to stabilize the typical chalice-shaped GM1 dimer, which serves as a landing platform for the SARS-CoV-2 spike protein (Fig. 6).
T137 529-765 Sentence denotes Moreover, the histograms of Fig. 5 show that all amino acid residues of the spike protein that are involved in ATM binding, including the QFN triad, are also essential for GM1 binding in the lipid raft environment (Table S1 and Fig. 5).
T138 766-933 Sentence denotes Taken together, these data indicate that the NTD of the viral glycoprotein may display a common ganglioside/ATM binding site, in agreement with our working hypothesis.
T139 934-1132 Sentence denotes Sequence alignments revealed that this common binding site, including the QFN triad, is totally conserved among clinical isolates of SARS-CoV-2 from various geographical origins worldwide (Fig. 7 ).
T140 1133-1315 Sentence denotes It is also conserved in bat RaTG13, which further illustrates the close relationship between this bat coronavirus and the SARS-CoV-2 strains that are currently circulating the world.
T141 1316-1404 Sentence denotes This region of the NTD should therefore be considered for SARS-CoV-2 vaccine strategies.
T142 1405-1655 Sentence denotes However, the motif has a different sequence signature in other animal- and human-related SARS coronaviruses (Fig. 7), indicating a recent evolution that may be linked to the higher contagiousness of SARS-CoV-2 compared with other human coronaviruses.
T143 1656-1734 Sentence denotes Fig. 6 MD simulations of GM1-spike protein interaction in a lipid raft domain.
T144 1735-1832 Sentence denotes Two GM1 gangliosides were merged with eight cholesterol (chol) and two sphingomyelin (SM) lipids.
T145 1833-1896 Sentence denotes After initial docking, MD simulations were performed for 50 ns.
T146 1897-1941 Sentence denotes Two distinct views of the complex are shown.
T147 1942-2037 Sentence denotes Cholesterol and sphingomyelin stabilize a dimer of GM1 clamped by the NTD of the spike protein.
T148 2038-2146 Sentence denotes Fig. 7 Amino acid sequence alignments of the ganglioside/ATM binding domain of the SARS-CoV-2 spike protein.
T149 2147-2311 Sentence denotes The first group of sequences includes clinical SARS-CoV-2 isolates from various geographical origins aligned with the reference sequence (6VSB_A, fragment 111-162).
T150 2312-2351 Sentence denotes The QFN triad is highlighted in yellow.
T151 2352-2441 Sentence denotes The second group of sequences includes human and animal viruses compared with SARS-CoV-2.
T152 2442-2584 Sentence denotes Deletions are highlighted in green, amino acid changes are highlighted in blue, conserved residues of the QFN triad are highlighted in yellow.
T153 2585-2934 Sentence denotes The degree of conservation observed in each column is symbolized by an asterisk (*) when the residue is fully conserved, a colon (:) for distinct residues with strongly similar properties (scoring > 0.5 in the Gonnet PAM 250 matrix), and a period (.) for distinct residues with weakly similar properties (scoring ≤ 0.5 in the Gonnet PAM 250 matrix).

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
457 2023-2028 Gene denotes spike Gene:43740568
458 1681-1684 Chemical denotes GM1 MESH:D005677
459 1716-1721 Chemical denotes lipid MESH:D008055
460 1739-1742 Chemical denotes GM1 MESH:D005677
461 1743-1755 Chemical denotes gangliosides MESH:D005732
462 1779-1790 Chemical denotes cholesterol MESH:D002784
463 1792-1796 Chemical denotes chol MESH:D002784
464 1806-1819 Chemical denotes sphingomyelin MESH:D013109
465 1821-1823 Chemical denotes SM MESH:D013109
466 1825-1831 Chemical denotes lipids MESH:D008055
467 1942-1953 Chemical denotes Cholesterol MESH:D002784
468 1958-1971 Chemical denotes sphingomyelin MESH:D013109
469 1993-1996 Chemical denotes GM1 MESH:D005677
477 2132-2137 Gene denotes spike Gene:43740568
478 2121-2131 Species denotes SARS-CoV-2 Tax:2697049
479 2194-2204 Species denotes SARS-CoV-2 Tax:2697049
480 2391-2396 Species denotes human Tax:9606
481 2430-2440 Species denotes SARS-CoV-2 Tax:2697049
482 2083-2094 Chemical denotes ganglioside MESH:D005732
483 2548-2551 Chemical denotes QFN
510 505-510 Gene denotes spike Gene:43740568
511 605-610 Gene denotes spike Gene:43740568
512 79-84 Gene denotes spike Gene:43740568
513 494-504 Species denotes SARS-CoV-2 Tax:2697049
514 1067-1077 Species denotes SARS-CoV-2 Tax:2697049
515 1231-1246 Species denotes bat coronavirus Tax:1508220
516 1255-1265 Species denotes SARS-CoV-2 Tax:2697049
517 1374-1384 Species denotes SARS-CoV-2 Tax:2697049
518 1480-1485 Species denotes human Tax:9606
519 1494-1512 Species denotes SARS coronaviruses Tax:694009
520 1604-1614 Species denotes SARS-CoV-2 Tax:2697049
521 1635-1640 Species denotes human Tax:9606
522 1641-1654 Species denotes coronaviruses Tax:11118
523 67-78 Chemical denotes ganglioside MESH:D005732
524 147-163 Chemical denotes GM1 gangliosides MESH:D005677
525 191-197 Chemical denotes lipids MESH:D008055
526 204-217 Chemical denotes sphingomyelin MESH:D013109
527 222-233 Chemical denotes cholesterol MESH:D002784
528 334-346 Chemical denotes gangliosides MESH:D005732
529 361-372 Chemical denotes cholesterol MESH:D002784
530 377-390 Chemical denotes sphingomyelin MESH:D013109
531 440-443 Chemical denotes GM1 MESH:D005677
532 701-704 Chemical denotes GM1 MESH:D005677
533 720-725 Chemical denotes lipid MESH:D008055
534 862-873 Chemical denotes ganglioside MESH:D005732
535 874-877 Chemical denotes ATM MESH:D017963