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PMC:7094172 / 13328-17853 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T715 537-545 SP_9 denotes MERS-CoV
T714 546-555 PG_4 denotes N protein
T713 596-604 SP_9 denotes MERS-CoV
T712 605-614 PG_4 denotes N protein
T711 770-779 PG_4 denotes N protein
T710 793-800 GO:0032991 denotes complex
T709 885-894 PG_4 denotes N protein
T708 912-919 GO:0032991 denotes complex
T707 1012-1021 PG_4 denotes N protein
T706 1039-1046 GO:0032991 denotes complex
T705 1260-1268 SP_9 denotes MERS-CoV
T704 1269-1278 PG_4 denotes N protein
T703 1352-1356 CHEBI:9754;CHEBI:9754 denotes Tris
T702 1357-1360 CHEBI:17883;CHEBI:17883 denotes HCl
T701 1369-1373 CHEBI:26710;CHEBI:26710 denotes NaCl
T700 1534-1546 GO:0046983 denotes dimerization
T699 1578-1590 GO:0046983 denotes dimerization
T698 1693-1702 PG_4 denotes N protein
T697 1806-1813 SO:0000409 denotes surface
T696 1866-1883 GO:0005840 denotes ribonucleocapsids
T272 31-39 SP_9 denotes MERS-CoV
T271 40-49 PG_4 denotes N Protein
T270 122-130 SP_9 denotes MERS-CoV
T269 131-140 PG_4 denotes N protein
T268 413-421 SP_9 denotes MERS-CoV
T267 422-431 PG_4 denotes N protein
T266 435-443 CHEBI:75958;CHEBI:75958 denotes solution
T265 1950-1959 PG_4 denotes N protein
T264 2105-2111 SO:0000417 denotes domain
T263 2159-2166 SO:0000417 denotes domains
T262 2246-2255 PG_4 denotes N protein
T261 2264-2271 GO:0032991 denotes complex
T260 2455-2464 PG_4 denotes N protein
T259 2526-2534 CHEBI:75958;CHEBI:75958 denotes solution
T258 2572-2580 CHEBI:75958;CHEBI:75958 denotes solution
T257 2669-2676 GO:0032991 denotes complex
T256 2967-2975 SP_9 denotes MERS-CoV
T255 2976-2985 PG_4 denotes N protein
T254 3053-3062 PG_4 denotes N protein
T253 3257-3269 GO:0046983 denotes dimerization
T252 3280-3288 SP_9 denotes MERS-CoV
T251 3304-3313 PG_4 denotes N protein
T250 3327-3332 NCBITaxon:10239 denotes viral
T249 3333-3339 SO:0001026 denotes genome
T248 3348-3351 GO:1990904 denotes RNP
T247 3352-3359 GO:0005662 denotes complex
T246 3730-3733 SO:0000694 denotes RNP
T245 4366-4375 PG_4 denotes N protein
T244 4376-4385 CHEBI:36357;CHEBI:36357 denotes molecules
T243 4468-4476 SP_9 denotes MERS-CoV
T242 4503-4512 PG_4 denotes N protein

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T54 42-49 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T55 133-140 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T56 201-208 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T57 299-305 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463
T58 330-337 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T59 424-431 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T60 548-555 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T61 607-614 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T62 719-725 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463
T63 772-779 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T64 887-894 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T65 1014-1021 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T66 1271-1278 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T67 1460-1463 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T68 1467-1475 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T69 1667-1674 Body_part denotes cuboids http://purl.org/sig/ont/fma/fma24527
T70 1695-1702 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T71 1794-1797 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T72 1952-1959 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T73 2054-2058 Body_part denotes body http://purl.org/sig/ont/fma/fma256135
T74 2248-2255 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T75 2378-2385 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T76 2457-2464 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T77 2648-2656 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T78 2978-2985 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T79 3055-3062 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T80 3163-3170 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T81 3306-3313 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T82 3333-3339 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T83 3551-3557 Body_part denotes cuboid http://purl.org/sig/ont/fma/fma24527
T84 3588-3591 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T85 3688-3694 Body_part denotes cuboid http://purl.org/sig/ont/fma/fma24527
T86 3779-3782 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T87 3905-3911 Body_part denotes cuboid http://purl.org/sig/ont/fma/fma24527
T88 3934-3937 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T89 4121-4128 Body_part denotes cuboids http://purl.org/sig/ont/fma/fma24527
T90 4244-4251 Body_part denotes cuboids http://purl.org/sig/ont/fma/fma24527
T91 4305-4308 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T92 4368-4375 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T93 4505-4512 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p35813s5 3045-3052 NegReg denotes delayed
p35813s6 3053-3083 MPA denotes N protein thermal denaturation

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T57 1127-1130 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T59 2113-2116 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T61 2504-2507 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T63 2795-2798 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T65 3253-3256 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T67 4034-4037 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
T94 354-355 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T95 374-375 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T96 558-561 http://purl.obolibrary.org/obo/CLO_0051456 denotes A–E
T97 617-618 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T98 760-761 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T99 852-853 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T100 896-897 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T101 1242-1244 http://purl.obolibrary.org/obo/CLO_0003358 denotes FL
T102 1323-1324 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 1476-1484 http://purl.obolibrary.org/obo/OBI_0000245 denotes organize
T104 1476-1484 http://purl.obolibrary.org/obo/OBI_0100026 denotes organize
T105 1476-1484 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organize
T106 1488-1489 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 2248-2271 http://purl.obolibrary.org/obo/GO_0043234 denotes protein and its complex
T108 2472-2473 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T109 2684-2685 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 2711-2712 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T111 2765-2766 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 2904-2905 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T113 3534-3539 http://purl.obolibrary.org/obo/UBERON_0001456 denotes faces
T114 3665-3670 http://purl.obolibrary.org/obo/UBERON_0001456 denotes faces
T115 4163-4164 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T116 4260-4261 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T111 42-49 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T112 133-140 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T113 201-208 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T114 319-321 Chemical denotes Rg http://purl.obolibrary.org/obo/CHEBI_33368
T115 330-337 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T116 424-431 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T117 435-443 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T118 548-555 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T119 607-614 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T120 772-779 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T121 887-894 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T122 1014-1021 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T123 1242-1244 Chemical denotes FL http://purl.obolibrary.org/obo/CHEBI_91150
T124 1271-1278 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T125 1325-1331 Chemical denotes buffer http://purl.obolibrary.org/obo/CHEBI_35225
T126 1352-1356 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T127 1357-1360 Chemical denotes HCl http://purl.obolibrary.org/obo/CHEBI_17883
T128 1369-1373 Chemical denotes NaCl http://purl.obolibrary.org/obo/CHEBI_26710
T129 1467-1475 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T130 1695-1702 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T131 1952-1959 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T132 2177-2179 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T133 2248-2255 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T134 2378-2385 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T135 2457-2464 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T136 2526-2534 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T137 2572-2580 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T138 2648-2656 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T139 2864-2870 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T140 2978-2985 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T141 3055-3062 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T142 3163-3170 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T143 3306-3313 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T144 4095-4097 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T145 4368-4375 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T146 4376-4385 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T147 4505-4512 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T13 1841-1850 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T14 3428-3437 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T15 4420-4429 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T16 4481-4490 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T107 0-61 Sentence denotes Structural Model of P3-Induced MERS-CoV N Protein Aggregation
T108 62-151 Sentence denotes We used SAXS to assess the effects of P3 on the full-length MERS-CoV N protein structure.
T109 152-252 Sentence denotes The fitted distance distribution function of the protein with and without P3 are shown in Figure 3A.
T110 253-390 Sentence denotes P3 increased the maximum dimension (Dmax) and radius of gyration (Rg) of the protein from 207 to 230 Å and from 58 to 65 Å, respectively.
T111 391-475 Sentence denotes Thus, the size of the MERS-CoV N protein in solution was altered upon binding to P3.
T112 476-714 Sentence denotes Figure 3 P3-induced abnormal aggregation on the full-length MERS-CoV N protein. (A–E) SAXS analysis of the full-length MERS-CoV N protein. (A) Normalized results from GNOM showing pairwise distance distribution P(r) and maximum distance.
T113 715-1100 Sentence denotes The radius of gyration fitted to 207 and 230 Å for the N protein and the N-P3 complex, respectively. “r” represents pairwise distances. (B, C) Scattering profiles of the N protein (B) and the N-P3 complex (C) and normalization fitting with GNOM (dashed lines). (D, E) Representative models of the N protein (D) and the N-P3 complex (E) generated by CRYSOL simulations of the SAXS data.
T114 1101-1126 Sentence denotes Only α carbons are shown.
T115 1127-1429 Sentence denotes NTD (yellow), CTD (green), and disorder region (cyan). (F, G) Conformation (F) and stability (G) analyses based on FL spectra of the MERS-CoV N protein (1 μM) incubated with P3 (10 μM) for 1 h in a buffer consisting of 50 mM Tris-HCl, 150 mM NaCl (pH 8.3). (H) Schematic of the P3 inhibition mechanism.
T116 1430-1547 Sentence denotes Left panel: in the absence of RNA, N proteins organize as a dimeric building block contributed by N-CTD dimerization.
T117 1548-1724 Sentence denotes Middle panel: P3 promoted the dimerization of N-NTDs from different building blocks, by which the distance between CTD cuboids was shortened and N protein aggregation occurred.
T118 1725-1824 Sentence denotes Right panel: octameric conformation of building blocks buried in the RNA-binding surface of N-CTDs.
T119 1825-1884 Sentence denotes It hindered the formation of filamentous ribonucleocapsids.
T120 1885-2030 Sentence denotes The presence of multiple intrinsically disordered regions in the N protein precluded the determination of its structure by X-ray crystallography.
T121 2031-2180 Sentence denotes Instead, we used rigid body modeling of the SAXS data with the N-terminal domain (NTD; solved in this study) and the C-terminal domains (CTD, PDB ID:
T122 2181-2294 Sentence denotes 6G13).23 In this way, we obtained structural models for the free N protein and its complex with P3 (Figure 3B,C).
T123 2295-2324 Sentence denotes Excellent fits were obtained.
T124 2325-2445 Sentence denotes Representative structural models for the full-length protein without and with P3 are shown in Figure 3D,E, respectively.
T125 2446-2547 Sentence denotes The free N protein formed a tetramer through CTD with the NTD freely hanging in solution (Figure 3D).
T126 2548-2748 Sentence denotes The conformation of the solution was consistent with structures previously reported for other CoV N proteins.33 The N-P3 complex formed a compact hexadecamer with a sunburst configuration (Figure 3E).
T127 2749-2847 Sentence denotes The CTDs formed a central ring and non-native NTD dimers formed “spikes” protruding from the ring.
T128 2848-3020 Sentence denotes Consistent with ligand-induced aggregation, we observed a “blue shift” in the fluorescence spectrum of the full-length MERS-CoV N protein in the presence of P3 (Figure 3F).
T129 3021-3223 Sentence denotes The addition of P3 also delayed N protein thermal denaturation and changed the shape of the denaturation curve, further suggesting that large protein aggregates formed in the presence of P3 (Figure 3G).
T130 3224-3299 Sentence denotes The structure explains how N-NTD dimerization decreased MERS-CoV viability.
T131 3300-3360 Sentence denotes The N protein packages the viral genome into an RNP complex.
T132 3361-3620 Sentence denotes Several models for N-CTD dimer assembly have been proposed for the formation of filamentous RNPs.33 All of the proposed interfaces between N-CTD dimers occurred on the side-faces of the CTD cuboid perpendicular to the proposed RNA-binding surface (Figure 3H).
T133 3621-3912 Sentence denotes Combinatorial use of any region on the side-faces of the CTD dimer cuboid may facilitate manipulation of the RNP length and curvature without obstructing the RNA-binding surface.28,34 However, the SAXS results indicated that N-CTD aggregation occurred on the β-sheet floor of the CTD cuboid.
T134 3913-4099 Sentence denotes For this reason, the RNA-binding surface of the CTD is occluded by the neighboring CTD on the ring and by the non-native NTD dimer making direct contact with the CTD (Figures 3H and S3).
T135 4100-4283 Sentence denotes In addition, the CTD cuboids in the aggregation naturally form a topologically closed octamer, leaving no open ends for further addition of CTD cuboids to form a long filamentous RNP.
T136 4284-4441 Sentence denotes Both the loss of the RNA-binding surface and the inability to incorporate further N protein molecules beyond an octamer may inhibit the formation of the RNP.
T137 4442-4525 Sentence denotes Therefore, P3 may inhibit MERS-CoV RNP formation by inducing N protein aggregation.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
208 20-22 Chemical denotes P3
209 31-61 Disease denotes MERS-CoV N Protein Aggregation MESH:C000657245
214 122-130 Species denotes MERS-CoV Tax:1335626
215 413-421 Species denotes MERS-CoV Tax:1335626
216 226-228 Chemical denotes P3
217 472-474 Chemical denotes P3
233 537-545 Species denotes MERS-CoV Tax:1335626
234 596-604 Species denotes MERS-CoV Tax:1335626
235 1260-1268 Species denotes MERS-CoV Tax:1335626
236 486-488 Chemical denotes P3
237 788-792 Chemical denotes N-P3
238 907-911 Chemical denotes N-P3
239 1034-1038 Chemical denotes N-P3
240 1108-1115 Chemical denotes carbons MESH:D002244
241 1301-1303 Chemical denotes P3
242 1352-1360 Chemical denotes Tris-HCl
243 1369-1373 Chemical denotes NaCl MESH:D012965
244 1562-1564 Chemical denotes P3
245 1594-1600 Chemical denotes N-NTDs
246 1817-1823 Chemical denotes N-CTDs
247 497-517 Disease denotes abnormal aggregation MESH:D001791
264 3348-3351 Gene denotes RNP Gene:55599
265 4477-4480 Gene denotes RNP Gene:55599
266 4437-4440 Gene denotes RNP Gene:55599
267 4279-4282 Gene denotes RNP Gene:55599
268 3730-3733 Gene denotes RNP Gene:55599
269 2642-2645 Species denotes CoV Tax:11118
270 2967-2975 Species denotes MERS-CoV Tax:1335626
271 3280-3288 Species denotes MERS-CoV Tax:1335626
272 4468-4476 Species denotes MERS-CoV Tax:1335626
273 2664-2668 Chemical denotes N-P3
274 3037-3039 Chemical denotes P3
275 3208-3210 Chemical denotes P3
276 3251-3256 Chemical denotes N-NTD
277 3380-3385 Chemical denotes N-CTD
278 2305-2309 Disease denotes fits MESH:D012640
279 3846-3863 Disease denotes N-CTD aggregation MESH:D001791

2_test

Id Subject Object Predicate Lexical cue
32105468-30644840-61929510 2187-2189 30644840 denotes 23
32105468-28044277-61929511 2657-2659 28044277 denotes 33
32105468-28044277-61929512 3458-3460 28044277 denotes 33
32105468-16775348-61929513 3799-3801 16775348 denotes 28
32105468-17379242-61929514 3802-3804 17379242 denotes 34