PMC:7556165 / 38969-41200
Annnotations
LitCovid-sample-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T146 | 187-194 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
T147 | 869-876 | Chemical | denotes | peptide | http://purl.obolibrary.org/obo/CHEBI_16670 |
LitCovid-sample-PD-NCBITaxon
Id | Subject | Object | Predicate | Lexical cue | ncbi_taxonomy_id |
---|---|---|---|---|---|
T169 | 37-45 | Species | denotes | SARS-CoV | NCBItxid:694009 |
T170 | 37-41 | Species | denotes | SARS | NCBItxid:694009 |
T171 | 50-60 | Species | denotes | SARS-CoV-2 | NCBItxid:2697049 |
T172 | 50-54 | Species | denotes | SARS | NCBItxid:694009 |
LitCovid-sample-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T240 | 0-225 | Sentence | denotes | To date, the cell entry mechanism of SARS-CoV and SARS-CoV-2 has been understood in its general details and it is based on a concerted action of receptor binding and proteolysis of the S protein (Figure 5; Tang et al., 2020). |
T241 | 226-417 | Sentence | denotes | Ultrastructural studies showed a metastable “prefusion” V-shaped trimer composed by three S1 heads sitting on top of a trimeric S2 stalk anchored into the virus membrane (Walls et al., 2016). |
T242 | 418-635 | Sentence | denotes | The RBD constantly switches between a standing-up (“open”) position for receptor binding and a lying-down (“closed”) configuration, the latter allowing immune evasion (Figure 6; Song et al., 2018; Wrapp et al., 2020). |
T243 | 636-754 | Sentence | denotes | Yet only one of the three RBD in trimeric S can flip up at a time and interact with the receptor (Wrapp et al., 2020). |
T244 | 755-917 | Sentence | denotes | The second key feature of the fusion mechanism is “priming” by host proteases, which recognize and cleave a short peptide motif at the S1/S2 boundary (Figure 4B). |
T245 | 918-1281 | Sentence | denotes | This cleavage does not disassemble S1 from S2 in pre-fusion conditions (Belouzard et al., 2009), but the binding interaction of RBD with its receptor, accompanied by a further cleavage in a second site in S2 (S2’site, upstream of FP, Figure 4B), triggers the possible dissociation of S1 and the irreversible refolding of S2 into a “post-fusion” state (Figure 4B). |
T246 | 1282-1517 | Sentence | denotes | In detail, HR1 undergoes a dramatic “jack-knife” conformational change, converting four helical stretches that run in an antiparallel fashion into a single long (∼130 aa) α-helix (Heald-Sargent and Gallagher, 2012; Walls et al., 2017). |
T247 | 1518-1632 | Sentence | denotes | At first, three of these helices assemble into a homotrimeric bundle and stick the FP into the host cell membrane. |
T248 | 1633-1787 | Sentence | denotes | Then, HR2 (one for each S2 chain) fold backward and bind to HR1, yielding the “six-helix bundle fusion core” (6-HB) of post-fusion S2 (Song et al., 2018). |
T249 | 1788-2020 | Sentence | denotes | This conformational foldback brings the FP (at N-terminus of HR1) and the TM (at the C terminus of HR2) close to each other, so that the viral and host cell membranes approach until their outer leaflets merge (hemifusion, Figure 5). |
T250 | 2021-2231 | Sentence | denotes | Eventually the inner leaflets merge (pore formation), enabling a connection between the interior of the virus and the host cell cytoplasm, that allows the delivery of viral genome (Figure 5; Tang et al., 2020). |
LitCovid-sample-PD-UBERON
Id | Subject | Object | Predicate | Lexical cue | uberon_id |
---|---|---|---|---|---|
T135 | 1455-1460 | Body_part | denotes | helix | http://purl.obolibrary.org/obo/UBERON_0002488 |
T136 | 1716-1721 | Body_part | denotes | helix | http://purl.obolibrary.org/obo/UBERON_0002488 |
T137 | 2058-2062 | Body_part | denotes | pore | http://purl.obolibrary.org/obo/UBERON_0008915 |
LitCovid-sample-Pubtator
Id | Subject | Object | Predicate | Lexical cue | pubann:denotes |
---|---|---|---|---|---|
1109 | 678-679 | Gene | denotes | S | Gene:43740568 |
1110 | 185-186 | Gene | denotes | S | Gene:43740568 |
1111 | 1752-1756 | Gene | denotes | post | Gene:159371 |
1112 | 1250-1254 | Gene | denotes | post | Gene:159371 |
1113 | 1623-1631 | Gene | denotes | membrane | Gene:43740571 |
1114 | 387-395 | Gene | denotes | membrane | Gene:43740571 |
1115 | 37-45 | Species | denotes | SARS-CoV | Tax:694009 |
1116 | 50-60 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
1117 | 1449-1451 | Gene | denotes | aa | Gene:351 |
LitCovid-sample-UniProt
Id | Subject | Object | Predicate | Lexical cue | uniprot_id |
---|---|---|---|---|---|
T3176 | 185-194 | Protein | denotes | S protein | https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9 |
T3209 | 422-425 | Protein | denotes | RBD | https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022 |
T3218 | 662-665 | Protein | denotes | RBD | https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022 |
T3227 | 1046-1049 | Protein | denotes | RBD | https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022 |
LitCovid-sample-PD-IDO
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T141 | 13-17 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell |
T142 | 381-386 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
T143 | 818-822 | http://purl.obolibrary.org/obo/IDO_0000531 | denotes | host |
T144 | 1115-1119 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | site |
T145 | 1130-1134 | http://purl.obolibrary.org/obo/BFO_0000029 | denotes | site |
T146 | 1613-1617 | http://purl.obolibrary.org/obo/IDO_0000531 | denotes | host |
T147 | 1618-1622 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell |
T148 | 1935-1939 | http://purl.obolibrary.org/obo/IDO_0000531 | denotes | host |
T149 | 1940-1944 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell |
T150 | 2125-2130 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
T151 | 2139-2143 | http://purl.obolibrary.org/obo/IDO_0000531 | denotes | host |
T152 | 2144-2148 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell |
LitCovid-sample-PD-FMA
Id | Subject | Object | Predicate | Lexical cue | fma_id |
---|---|---|---|---|---|
T330 | 13-17 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
T331 | 187-194 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
T332 | 1455-1460 | Body_part | denotes | helix | http://purl.org/sig/ont/fma/fma60992 |
T333 | 1618-1631 | Body_part | denotes | cell membrane | http://purl.org/sig/ont/fma/fma63841 |
T334 | 1618-1622 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
T335 | 1716-1721 | Body_part | denotes | helix | http://purl.org/sig/ont/fma/fma60992 |
T336 | 1940-1954 | Body_part | denotes | cell membranes | http://purl.org/sig/ont/fma/fma63841 |
T337 | 1940-1944 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
T338 | 2144-2148 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
T339 | 2149-2158 | Body_part | denotes | cytoplasm | http://purl.org/sig/ont/fma/fma66835 |
T340 | 2194-2200 | Body_part | denotes | genome | http://purl.org/sig/ont/fma/fma84116 |
LitCovid-sample-PD-MONDO
Id | Subject | Object | Predicate | Lexical cue | mondo_id |
---|---|---|---|---|---|
T158 | 37-45 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T159 | 37-41 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
T160 | 50-60 | Disease | denotes | SARS-CoV-2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
T161 | 50-54 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-sample-PD-MAT
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T125 | 319-324 | http://purl.obolibrary.org/obo/MAT_0000294 | denotes | heads |
LitCovid-sample-PD-GO-BP-0
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T91 | 166-177 | http://purl.obolibrary.org/obo/GO_0006508 | denotes | proteolysis |
T92 | 570-584 | http://purl.obolibrary.org/obo/GO_0020012 | denotes | immune evasion |
T93 | 570-584 | http://purl.obolibrary.org/obo/GO_0051805 | denotes | immune evasion |
T94 | 2058-2072 | http://purl.obolibrary.org/obo/GO_0046931 | denotes | pore formation |
T95 | 2063-2072 | http://purl.obolibrary.org/obo/GO_0009058 | denotes | formation |
LitCovid-sample-GO-BP
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T94 | 166-177 | http://purl.obolibrary.org/obo/GO_0006508 | denotes | proteolysis |
T95 | 570-584 | http://purl.obolibrary.org/obo/GO_0042783 | denotes | immune evasion |
T96 | 2058-2072 | http://purl.obolibrary.org/obo/GO_0046931 | denotes | pore formation |
T97 | 2063-2072 | http://purl.obolibrary.org/obo/GO_0009058 | denotes | formation |
LitCovid-PubTator
Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
---|---|---|---|---|---|
1109 | 678-679 | Gene | denotes | S | Gene:43740568 |
1110 | 185-186 | Gene | denotes | S | Gene:43740568 |
1111 | 1752-1756 | Gene | denotes | post | Gene:159371 |
1112 | 1250-1254 | Gene | denotes | post | Gene:159371 |
1113 | 1623-1631 | Gene | denotes | membrane | Gene:43740571 |
1114 | 387-395 | Gene | denotes | membrane | Gene:43740571 |
1115 | 37-45 | Species | denotes | SARS-CoV | Tax:694009 |
1116 | 50-60 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
1117 | 1449-1451 | Gene | denotes | aa | Gene:351 |
LitCovid-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T240 | 0-225 | Sentence | denotes | To date, the cell entry mechanism of SARS-CoV and SARS-CoV-2 has been understood in its general details and it is based on a concerted action of receptor binding and proteolysis of the S protein (Figure 5; Tang et al., 2020). |
T241 | 226-417 | Sentence | denotes | Ultrastructural studies showed a metastable “prefusion” V-shaped trimer composed by three S1 heads sitting on top of a trimeric S2 stalk anchored into the virus membrane (Walls et al., 2016). |
T242 | 418-635 | Sentence | denotes | The RBD constantly switches between a standing-up (“open”) position for receptor binding and a lying-down (“closed”) configuration, the latter allowing immune evasion (Figure 6; Song et al., 2018; Wrapp et al., 2020). |
T243 | 636-754 | Sentence | denotes | Yet only one of the three RBD in trimeric S can flip up at a time and interact with the receptor (Wrapp et al., 2020). |
T244 | 755-917 | Sentence | denotes | The second key feature of the fusion mechanism is “priming” by host proteases, which recognize and cleave a short peptide motif at the S1/S2 boundary (Figure 4B). |
T245 | 918-1281 | Sentence | denotes | This cleavage does not disassemble S1 from S2 in pre-fusion conditions (Belouzard et al., 2009), but the binding interaction of RBD with its receptor, accompanied by a further cleavage in a second site in S2 (S2’site, upstream of FP, Figure 4B), triggers the possible dissociation of S1 and the irreversible refolding of S2 into a “post-fusion” state (Figure 4B). |
T246 | 1282-1517 | Sentence | denotes | In detail, HR1 undergoes a dramatic “jack-knife” conformational change, converting four helical stretches that run in an antiparallel fashion into a single long (∼130 aa) α-helix (Heald-Sargent and Gallagher, 2012; Walls et al., 2017). |
T247 | 1518-1632 | Sentence | denotes | At first, three of these helices assemble into a homotrimeric bundle and stick the FP into the host cell membrane. |
T248 | 1633-1787 | Sentence | denotes | Then, HR2 (one for each S2 chain) fold backward and bind to HR1, yielding the “six-helix bundle fusion core” (6-HB) of post-fusion S2 (Song et al., 2018). |
T249 | 1788-2020 | Sentence | denotes | This conformational foldback brings the FP (at N-terminus of HR1) and the TM (at the C terminus of HR2) close to each other, so that the viral and host cell membranes approach until their outer leaflets merge (hemifusion, Figure 5). |
T250 | 2021-2231 | Sentence | denotes | Eventually the inner leaflets merge (pore formation), enabling a connection between the interior of the virus and the host cell cytoplasm, that allows the delivery of viral genome (Figure 5; Tang et al., 2020). |