PMC:7443692 / 32629-35543
Annnotations
LitCovid-sample-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T189 | 120-127 | Chemical | denotes | Protein | http://purl.obolibrary.org/obo/CHEBI_16541 |
| T190 | 132-138 | Chemical | denotes | Glycan | http://purl.obolibrary.org/obo/CHEBI_18154 |
| T191 | 612-619 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T192 | 718-725 | Chemical | denotes | glycans | http://purl.obolibrary.org/obo/CHEBI_18154 |
| T193 | 884-891 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T194 | 1545-1552 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T195 | 2110-2117 | Chemical | denotes | glycans | http://purl.obolibrary.org/obo/CHEBI_18154 |
| T196 | 2159-2166 | Chemical | denotes | glycans | http://purl.obolibrary.org/obo/CHEBI_18154 |
| T197 | 2202-2209 | Chemical | denotes | glycans | http://purl.obolibrary.org/obo/CHEBI_18154 |
| T198 | 2393-2400 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T199 | 2498-2505 | Chemical | denotes | glycans | http://purl.obolibrary.org/obo/CHEBI_18154 |
LitCovid-sample-PD-NCBITaxon
| Id | Subject | Object | Predicate | Lexical cue | ncbi_taxonomy_id |
|---|---|---|---|---|---|
| T89 | 50-60 | Species | denotes | SARS-CoV-2 | NCBItxid:2697049 |
| T90 | 100-105 | Species | denotes | Human | NCBItxid:9606 |
| T91 | 550-560 | Species | denotes | SARS-CoV-2 | NCBItxid:2697049 |
| T92 | 1826-1831 | Species | denotes | Human | NCBItxid:9606 |
| T93 | 1854-1864 | Species | denotes | SARS-CoV-2 | NCBItxid:2697049 |
| T94 | 1980-1985 | Species | denotes | human | NCBItxid:9606 |
| T95 | 2008-2018 | Species | denotes | SARS-CoV-2 | NCBItxid:2697049 |
| T96 | 2534-2539 | Species | denotes | human | NCBItxid:9606 |
LitCovid-sample-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T198 | 0-151 | Sentence | denotes | MD Simulation of the Glycosylated Trimer Spike of SARS-CoV-2 in Complex with Glycosylated, Soluble, Human Ace 2 Reveals Protein and Glycan Interactions |
| T199 | 152-276 | Sentence | denotes | MD simulations were performed to examine the co-complex (generated from a crystal structure of the ACE2-RBD co-complex, PDB: |
| T200 | 277-459 | Sentence | denotes | 6M0J; Lan et al., 2020) of glycosylated S with glycosylated ACE2 with the three different glycoforms models (Abundance, Oxford Class, and Processed; Table S1; Videos S5, S6, and S7). |
| T201 | 460-698 | Sentence | denotes | Information from these analyses is laid out along the primary structure (sequence) of the SARS-CoV-2 S protomer and ACE2 highlighting regions of glycan-protein interaction observed in the MD simulations (Table S14; Videos S5, S6, and S7). |
| T202 | 699-904 | Sentence | denotes | Interestingly, two glycans on ACE2 (at N090 and N322), which are highlighted in Figure 7 A and shown in a more close-up view in Figure 7B, are predicted to form interactions with the S protein (Table S15). |
| T203 | 905-1127 | Sentence | denotes | The N322 glycan interaction with the S trimer is outside of the receptor-binding domain, and the interaction is observed across multiple simulations and throughout each simulation (Figures 7A and 7B; Video S5, S6, and S7). |
| T204 | 1128-1419 | Sentence | denotes | The ACE2 glycan at N090 is close enough to the S trimer surface to repeatedly form interactions; however, the glycan arms interact with multiple regions of the surface over the course of the simulations, reflecting the relatively high degree of glycan dynamics (Figures 7A and 7B; Video S3). |
| T205 | 1420-1604 | Sentence | denotes | Inter-molecule glycan-glycan interactions are also observed repeatedly between the glycan at N546 of ACE2 and those in the S protein at residues N0074 and N0165 (Figure 7D; Table S16). |
| T206 | 1605-1779 | Sentence | denotes | Finally, a full view of the ACE2-S complex with Oxford class glycoforms on ACE2 illustrates the extensive glycosylation at the interface of the complex (Figure 7C; Video S4). |
| T207 | 1780-1937 | Sentence | denotes | Figure 7 Interactions of Glycosylated Soluble Human ACE2 and Glycosylated SARS-CoV-2 S Trimer Immunogen Revealed By 3D-Structural Modeling and MD Simulations |
| T208 | 1938-2078 | Sentence | denotes | (A) MD simulation of glycosylated soluble human ACE2 and glycosylated SARS-CoV-2 S trimer immunogen interaction (see Videos S5, S6, and S7). |
| T209 | 2079-2180 | Sentence | denotes | ACE2 (top) is colored red with glycans in pink, whereas S is colored white with glycans in dark gray. |
| T210 | 2181-2263 | Sentence | denotes | Highlighted are ACE2 glycans that interact with S that are magnified to the right. |
| T211 | 2264-2453 | Sentence | denotes | (B) Magnification of ACE2-S interface highlighting ACE2 glycan interactions by using 3D-SNFG icons (Thieker et al., 2016) with S protein (pink) as well as ACE2-S glycan-glycan interactions. |
| T212 | 2454-2574 | Sentence | denotes | (C) Magnification of dynamics trajectory of glycans at the interface of soluble human ACE2 and S (see Videos S3 and S4). |
| T213 | 2575-2584 | Sentence | denotes | Video S3. |
| T214 | 2585-2634 | Sentence | denotes | Interface of ACE2-S Complex, Related to Figure 7C |
| T215 | 2635-2644 | Sentence | denotes | Video S4. |
| T216 | 2645-2698 | Sentence | denotes | The Glycosylated ACE2-S Complex, Related to Figure 7C |
| T217 | 2699-2708 | Sentence | denotes | Video S5. |
| T218 | 2709-2769 | Sentence | denotes | Abundance Glycoforms on ACE2-S Complex, Related to Figure 7A |
| T219 | 2770-2779 | Sentence | denotes | Video S6. |
| T220 | 2780-2843 | Sentence | denotes | Oxford Class Glycoforms on ACE2-S Complex, Related to Figure 7A |
| T221 | 2844-2853 | Sentence | denotes | Video S7. |
| T222 | 2854-2914 | Sentence | denotes | Processed Glycoforms on ACE2-S Complex, Related to Figure 7A |
LitCovid-sample-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T60 | 50-60 | Disease | denotes | SARS-CoV-2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T61 | 550-560 | Disease | denotes | SARS-CoV-2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T62 | 1854-1864 | Disease | denotes | SARS-CoV-2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T63 | 2008-2018 | Disease | denotes | SARS-CoV-2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
LitCovid-sample-UniProt
| Id | Subject | Object | Predicate | Lexical cue | uniprot_id |
|---|---|---|---|---|---|
| T2169 | 251-255 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2170 | 256-259 | 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 |
| T2179 | 337-341 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2180 | 576-580 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2181 | 670-673 | Protein | denotes | S14 | https://www.uniprot.org/uniprot/Q92748|https://www.uniprot.org/uniprot/Q63536|https://www.uniprot.org/uniprot/Q62264|https://www.uniprot.org/uniprot/P04143|https://www.uniprot.org/uniprot/B2R4W7 |
| T2186 | 729-733 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2187 | 882-891 | 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 |
| T2220 | 1132-1136 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2221 | 1521-1525 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2222 | 1543-1552 | 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 |
| T2255 | 1616-1620 | Protein | denotes | full | https://www.uniprot.org/uniprot/Q8N1N2 |
| T2256 | 1633-1637 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2257 | 1680-1684 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2258 | 1832-1836 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2259 | 1986-1990 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2260 | 2079-2083 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2261 | 2197-2201 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2262 | 2285-2289 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2263 | 2315-2319 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2264 | 2391-2400 | 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 |
| T2297 | 2419-2423 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2298 | 2540-2544 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2299 | 2598-2602 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2300 | 2662-2666 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2301 | 2733-2737 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2302 | 2807-2811 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
| T2303 | 2878-2882 | Protein | denotes | ACE2 | https://www.uniprot.org/uniprot/Q9UFZ6 |
LitCovid-sample-PD-FMA
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T99 | 120-127 | Body_part | denotes | Protein | http://purl.org/sig/ont/fma/fma67257 |
| T100 | 612-619 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T101 | 884-891 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T102 | 1545-1552 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T103 | 2393-2400 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
LitCovid-sample-PD-GO-BP-0
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T76 | 1711-1724 | http://purl.obolibrary.org/obo/GO_0070085 | denotes | glycosylation |
LitCovid-sample-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T72 | 1711-1724 | http://purl.obolibrary.org/obo/GO_0070085 | denotes | glycosylation |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32841605-32225176-19659521 | 295-299 | 32225176 | denotes | 2020 |
| 32841605-27514939-19659522 | 2380-2384 | 27514939 | denotes | 2016 |