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PMC:7556165 / 38969-41200 JSONTXT

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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).