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PMC:7094172 / 4762-10117 JSONTXT

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LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T669 3845-3853 SP_9 denotes MERS-CoV
T668 3890-3898 SP_9 denotes MERS-CoV
T667 4029-4041 GO:0046983 denotes dimerization
T666 4109-4117 SP_9 denotes MERS-CoV
T665 4126-4138 GO:0051260 denotes Dimerization
T664 4161-4167 SO:0000440 denotes vector
T663 4694-4700 SO:0000440 denotes vector
T662 4975-4981 SO:0000440 denotes vector
T661 5249-5267 SO:0000366 denotes substitution sites
T660 5309-5321 GO:0046983 denotes dimerization
T170 28-34 SO:0000417 denotes Domain
T169 42-50 SP_9 denotes MERS-CoV
T168 51-60 PG_4 denotes N Protein
T167 100-108 SP_9 denotes MERS-CoV
T166 395-404 CHEBI:36357;CHEBI:36357 denotes molecules
T165 621-634 SO:0000984 denotes five-stranded
T164 1049-1057 SP_9 denotes MERS-CoV
T163 1058-1067 PG_4 denotes N protein
T162 1178-1190 SO:0000409 denotes binding site
T161 1351-1360 PG_4 denotes N protein
T160 1480-1490 CHEBI:50325;CHEBI:50325 denotes side chain
T159 1708-1719 CHEBI:50325;CHEBI:50325 denotes side chains
T158 1970-1981 CHEBI:50325;CHEBI:50325 denotes side chains
T157 2066-2076 CHEBI:50325;CHEBI:50325 denotes side chain
T156 2537-2543 SO:0000440 denotes vector
T155 2746-2755 PG_4 denotes N protein
T154 2837-2841 SP_9 denotes MERS
T153 2863-2869 SO:0000440 denotes vector
T152 2889-2897 CHEBI:75958;CHEBI:75958 denotes solution
T151 2899-2903 SP_9 denotes MERS
T150 2940-2948 CHEBI:75958;CHEBI:75958 denotes solution
T149 3060-3066 SO:0000440 denotes vector
T148 3289-3295 SO:0000440 denotes vector
T147 3412-3420 SP_9 denotes MERS-CoV
T146 3521-3531 CHEBI:50325;CHEBI:50325 denotes side chain
T145 3705-3714 CHEBI:36357;CHEBI:36357 denotes compounds
T144 3730-3736 SO:0000440 denotes vector

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T32 53-60 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T33 695-707 Body_part denotes right-handed http://purl.org/sig/ont/fma/fma9713
T34 868-876 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T35 1060-1067 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T36 1148-1158 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T37 1353-1360 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T38 1778-1786 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T39 2291-2293 Body_part denotes Å2 http://purl.org/sig/ont/fma/fma66595
T40 2748-2755 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T41 3296-3304 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T42 4787-4794 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T43 5136-5144 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p35702s4 3167-3174 NegReg denotes reduced
p35702s6 3179-3198 MPA denotes oligomeric tendency
p35702s9 3202-3207 MPA denotes N-NTD

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T21 111-114 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T23 180-183 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T25 391-394 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T27 2844-2847 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T29 2906-2909 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T31 3114-3117 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T33 3204-3207 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T35 3423-3426 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T37 3856-3859 Disease denotes NTD http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075
T39 3901-3904 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
T31 141-143 http://purl.obolibrary.org/obo/CLO_0007860 denotes MR
T32 319-320 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 339-340 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T34 348-350 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T35 470-471 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T36 503-504 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T37 527-528 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 565-566 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 619-620 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 693-694 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 930-931 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 1434-1435 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 1533-1534 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 1798-1802 http://purl.obolibrary.org/obo/CLO_0001757 denotes 1 at
T45 1803-1804 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 1821-1822 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T47 2009-2013 http://purl.obolibrary.org/obo/CLO_0001757 denotes 1 at
T48 2045-2046 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T49 2105-2106 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 2167-2171 http://purl.obolibrary.org/obo/CLO_0001757 denotes 1 at
T51 2172-2173 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 2190-2191 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T53 2291-2293 http://purl.obolibrary.org/obo/CLO_0001562 denotes Å2
T54 2291-2293 http://purl.obolibrary.org/obo/CLO_0001563 denotes Å2
T55 2421-2422 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 2663-2666 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T57 2914-2915 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 3441-3443 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T59 3455-3456 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 3862-3863 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T61 3954-3955 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 4082-4088 http://purl.obolibrary.org/obo/CLO_0001869 denotes B). (B
T63 4369-4376 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T64 4583-4584 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T65 5014-5021 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T52 53-60 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T53 141-143 Chemical denotes MR http://purl.obolibrary.org/obo/CHEBI_74698
T54 189-191 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T55 395-404 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T56 868-876 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T57 1060-1067 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T58 1148-1158 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T59 1148-1153 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T60 1154-1158 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T61 1353-1360 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T62 1570-1573 Chemical denotes H37 http://purl.obolibrary.org/obo/CHEBI_34780
T63 1751-1759 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T64 1946-1954 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T65 2107-2115 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T66 2141-2147 Chemical denotes oxygen http://purl.obolibrary.org/obo/CHEBI_25805
T67 2561-2564 Chemical denotes H37 http://purl.obolibrary.org/obo/CHEBI_34780
T68 2748-2755 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T69 2889-2897 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T70 2940-2948 Chemical denotes solution http://purl.obolibrary.org/obo/CHEBI_75958
T71 3432-3434 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T72 3771-3774 Chemical denotes PPI http://purl.obolibrary.org/obo/CHEBI_53266|http://purl.obolibrary.org/obo/CHEBI_60614
T74 4787-4794 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T75 5136-5144 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T9 3124-3133 http://purl.obolibrary.org/obo/GO_0009058 denotes formation
T10 3318-3327 http://purl.obolibrary.org/obo/GO_0009058 denotes formation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T31 0-60 Sentence denotes Structure of the N-Terminal Domain of the MERS-CoV N Protein
T32 61-192 Sentence denotes We determined the crystal structure of MERS-CoV N-NTD by molecular replacement (MR) using the structure of HCoV-OC43 N-NTD (PDB ID:
T33 193-352 Sentence denotes 4J3K) as the search model.24 The final structure was refined to R-factor and R-free values of 0.26 and 0.29, respectively, at a resolution of 2.6 Å (Table S1).
T34 353-506 Sentence denotes Each asymmetric unit contained four N-NTD molecules assembled into two identical dimers with an overall RMSD of 0.28 Å between the dimers (Figure S1A,B).
T35 507-596 Sentence denotes The monomers shared a similar structural core preceded by a flexible region (Figure S1D).
T36 597-888 Sentence denotes The core consisted of a five-stranded antiparallel β-sheet sandwiched between loops arranged in a right-handed, fist-shaped structure conserved among the CoVs.25 In our structure, however, the loop connecting strands β2 and β3 protruding out of the core into other CoV N proteins was absent.
T37 889-993 Sentence denotes Unlike the reported structures that have a monomeric conformation, our structure was atypically dimeric.
T38 994-1074 Sentence denotes Figure 1B shows the details of the interactions in the MERS-CoV N protein dimer.
T39 1075-1130 Sentence denotes We named the units monomer 1 and monomer 2 (Figure 1A).
T40 1131-1361 Sentence denotes According to the amino acid composition of the binding site on monomer 2, we divided the dimeric interface into two areas: one located on the N-terminus flexible region and the other on the loop between β4 and β5 of the N protein.
T41 1362-1569 Sentence denotes In the first area, W43, N66, N68, Y102, and F135 of monomer 1 generated a conserved hydrophobic pocket permitting the side chain of M38 of monomer 2 to enter this hole by a hydrophobic contact (Figure 1C,D).
T42 1570-1703 Sentence denotes H37 and N39 of monomer 2 were packed against W43 and F135 of monomer 1, respectively, and contributed to the hydrophobic interaction.
T43 1704-1823 Sentence denotes The side chains of N39 of monomer 2 formed one hydrogen bond with the N68 backbone in monomer 1 at a distance of 2.6 Å.
T44 1824-1872 Sentence denotes The second area was relatively more hydrophilic.
T45 1873-2061 Sentence denotes The main chain oxygens of G104, F135, and T137 of monomer 2 formed three hydrogen bonds with the side chains of Q73 and T134 of monomer 1 at distances of 3.8, 3.2, and 3.7 Å, respectively.
T46 2062-2192 Sentence denotes The side chain of N139 on monomer 2 formed a hydrogen bond with the main chain oxygen of T137 on monomer 1 at a distance of 3.6 Å.
T47 2193-2308 Sentence denotes The interactions of the first and second areas comprise buried surface areas (BSA) of 289 and 103 Å2, respectively.
T48 2309-2456 Sentence denotes The small surface area buried at the interface accounts for ∼5 kcal mol–1 binding energy,26 which translates to a dissociation constant of ∼200 mM.
T49 2457-2605 Sentence denotes Thus, the dimer described here is unique in that it is non-native and relies on vector-fusion residues (H37 and M38) to maintain its dimeric status.
T50 2606-2898 Sentence denotes This property may also explain why the present structure has an oligomeric status different from previously reported structures for the CoV N protein.24,27−30 We used cross-linking experiments to analyze the oligomeric capacity of MERS N-NTD containing the vector-fusion residues in solution.
T51 2899-2949 Sentence denotes MERS N-NTD had a dimeric conformation in solution.
T52 2950-3134 Sentence denotes Our structure indicated that W43 played an essential role in forming the hydrophobic pocket accommodating the vector-fusion residues and, therefore, mediated the N-NTD dimer formation.
T53 3135-3221 Sentence denotes The W43A mutation significantly reduced the oligomeric tendency of N-NTD (Figure S1C).
T54 3222-3352 Sentence denotes This further supports that the “exogenous residues” encoded by the vector backbone mediated the formation of the non-native dimer.
T55 3353-3435 Sentence denotes We also superimposed the previously published structure of MERS-CoV N-NTD (PDB ID:
T56 3436-3516 Sentence denotes 4ud1)27 containing a native N-terminal flexible region with our dimer structure.
T57 3517-3662 Sentence denotes The side chain of N38 in the native structure could not interact with the hydrophobic pocket as the former is hydrophilic and short (Figure S1E).
T58 3663-3808 Sentence denotes Thus, it may be possible to utilize small compounds to replace the vector-fusion residues and stabilize the PPI through hydrophobic interactions.
T59 3809-4007 Sentence denotes Figure 1 Structure and sequence of MERS-CoV N-NTD. (A) Overall structure of the MERS-CoV N-NTD dimer containing monomers 1 and 2 is depicted as a cartoon and colored yellow and green, respectively.
T60 4008-4125 Sentence denotes Residues involved in dimerization are shown as sticks and highlighted in (B). (B) Interactions among MERS-CoV N-NTDs.
T61 4126-4323 Sentence denotes Dimerization is mediated mainly by vector-fusion residues interacting with the conserved hydrophobic regions on the core structure (first area) along with the residues surrounding it (second area).
T62 4324-4409 Sentence denotes Interacting residues on monomers 1 and 2 are labeled in black and blue, respectively.
T63 4410-4497 Sentence denotes Vector-fusion and conserved hydrophobic regions are colored cyan and red, respectively.
T64 4498-4586 Sentence denotes The color of all other interacting residues is the same as that for each monomer in (A).
T65 4587-4717 Sentence denotes Polar contacts are indicated with red dashed lines. (C) Upper panel: close-up of the interacting region of vector-fusion residues.
T66 4718-4803 Sentence denotes The surface was colored according to the hydrophobicity level at the protein surface.
T67 4804-4891 Sentence denotes Vector-fusion residues (black) are shown as sticks to emphasize the hydrophobic pocket.
T68 4892-4904 Sentence denotes Lower panel:
T69 4905-4998 Sentence denotes 2D diagrams of the interaction between the hydrophobic pocket and the vector-fusion residues.
T70 4999-5031 Sentence denotes The latter are labeled in black.
T71 5032-5170 Sentence denotes The hydrophobic contacts are indicated with black dashed lines. (D) Sequence alignment of various CoV N proteins in the N-terminal region.
T72 5171-5220 Sentence denotes Red letters indicate strictly conserved residues.
T73 5221-5268 Sentence denotes Cyan indicates conservative substitution sites.
T74 5269-5355 Sentence denotes Hydrophobic regions involved in unusual dimerization are indicated by black triangles.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
87 42-50 Species denotes MERS-CoV Tax:1335626
93 100-108 Species denotes MERS-CoV Tax:1335626
94 168-177 Species denotes HCoV-OC43 Tax:31631
95 751-755 Species denotes CoVs Tax:11118
96 862-865 Species denotes CoV Tax:11118
97 389-394 Chemical denotes N-NTD
111 1334-1336 Gene denotes β4 Gene:28898
112 1341-1343 Gene denotes β5 Gene:28884
113 1049-1057 Species denotes MERS-CoV Tax:1335626
114 2742-2745 Species denotes CoV Tax:11118
115 3412-3420 Species denotes MERS-CoV Tax:1335626
116 1751-1759 Chemical denotes hydrogen MESH:D006859
117 1774-1777 Chemical denotes N68 MESH:C495502
118 1888-1895 Chemical denotes oxygens MESH:D010100
119 1946-1954 Chemical denotes hydrogen MESH:D006859
120 2080-2084 Chemical denotes N139
121 2107-2115 Chemical denotes hydrogen MESH:D006859
122 2141-2147 Chemical denotes oxygen MESH:D010100
123 3112-3117 Chemical denotes N-NTD
131 3922-3938 Gene denotes monomers 1 and 2
132 4348-4364 Gene denotes monomers 1 and 2
133 3845-3853 Species denotes MERS-CoV Tax:1335626
134 3890-3898 Species denotes MERS-CoV Tax:1335626
135 5130-5133 Species denotes CoV Tax:11118
136 3899-3904 Chemical denotes N-NTD
137 4114-4124 Disease denotes CoV N-NTDs MESH:C000657245

2_test

Id Subject Object Predicate Lexical cue
32105468-16338414-61929504 756-758 16338414 denotes 25
32105468-23389845-61929505 2398-2400 23389845 denotes 26
32105468-26894667-61929506 2759-2761 26894667 denotes 27
32105468-19782089-61929507 2762-2764 19782089 denotes 30
32105468-26894667-61929508 3441-3443 26894667 denotes 27