SMTL ID : 9q1j.1

Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 E191A mutant-T20P14-R complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

2 x U- U- C- C- C- C: RNA (5'-R(*A*UP*UP*CP*CP*CP*C)-3')(Non-covalent)

U-U-C-C-C-C.1: 21 residues within 4Å: Chain D: D.90, V.91, E.92, G.93, H.95, N.104, P.141, F.146, W.186, A.187, Q.245, G.251, N.252, L.253 Chain E: G.1, G.2, G.3, A.4, A.5, U.6 Ligands: MG.11 9 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: D:G.6, D:N.104, D:N.104, D:N.104, C:A.1 Salt bridges: D:K.9, D:K.9, B:K.13, B:K.13 U-U-C-C-C-C.2: 21 residues within 4Å: Chain I: D.90, V.91, E.92, G.93, H.95, N.104, P.141, F.146, W.186, A.187, Q.245, G.251, N.252, L.253 Chain J: G.1, G.2, G.3, A.4, A.5, U.6 Ligands: MG.23 Protein-ligand interaction information (PLIP) not available

20 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.74, A:C.77, A:H.83, A:C.90 ZN.4: 4 residues within 4Å: Chain A: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.117, A:C.120, A:C.128, A:C.130 ZN.6: 4 residues within 4Å: Chain B: C.207, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.207, B:C.210, B:C.226, B:H.229 ZN.7: 4 residues within 4Å: Chain B: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.257, B:C.261, B:H.264, B:C.279 ZN.8: 4 residues within 4Å: Chain B: C.452, C.477, C.484, H.487 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.452, B:C.477, B:C.484, B:H.487 ZN.9: 4 residues within 4Å: Chain C: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.74, C:C.77, C:H.83, C:C.90 ZN.10: 4 residues within 4Å: Chain C: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.117, C:C.120, C:C.128, C:C.130 ZN.12: 4 residues within 4Å: Chain D: C.207, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.207, D:C.210, D:C.226, D:H.229 ZN.13: 4 residues within 4Å: Chain D: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.257, D:C.261, D:H.264, D:C.279 ZN.14: 4 residues within 4Å: Chain D: C.452, C.477, C.484, H.487 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.452, D:C.477, D:C.484, D:H.487 ZN.15: 4 residues within 4Å: Chain F: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.74, F:C.77, F:H.83, F:C.90 ZN.16: 4 residues within 4Å: Chain F: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.117, F:C.120, F:C.128, F:C.130 ZN.18: 4 residues within 4Å: Chain G: C.207, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.207, G:C.210, G:C.226, G:H.229 ZN.19: 4 residues within 4Å: Chain G: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.257, G:C.261, G:H.264, G:C.279 ZN.20: 4 residues within 4Å: Chain G: C.452, C.477, C.484, H.487 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.452, G:C.477, G:C.484, G:H.487 ZN.21: 4 residues within 4Å: Chain H: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.74, H:C.77, H:H.83, H:C.90 ZN.22: 4 residues within 4Å: Chain H: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.117, H:C.120, H:C.128, H:C.130 ZN.24: 4 residues within 4Å: Chain I: C.207, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.207, I:C.210, I:C.226, I:H.229 ZN.25: 4 residues within 4Å: Chain I: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.257, I:C.261, I:H.264, I:C.279 ZN.26: 4 residues within 4Å: Chain I: C.452, C.477, C.484, H.487 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.452, I:C.477, I:C.484, I:H.487

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: D.90, E.92, D.273 Chain E: X.39 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.90, B:D.90, B:E.92, B:D.273 MG.11: 4 residues within 4Å: Chain D: D.90, E.92, D.273 Ligands: U-U-C-C-C-C.1 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.90, D:E.92, D:D.273 MG.17: 4 residues within 4Å: Chain G: D.90, E.92, D.273 Chain J: X.39 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.90, G:D.90, G:E.92, G:D.273 MG.23: 4 residues within 4Å: Chain I: D.90, E.92, D.273 Ligands: U-U-C-C-C-C.2 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.90, I:E.92, I:D.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Molecular basis of SARS-CoV-2 proofreading enzyme-mediated resistance to remdesivir. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-09-24

Peptides

Non-structural protein 10: ACFH
Proofreading exoribonuclease: BDGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

F
G

H
I

B
B

D
D

G
H

I
J

Non-structural protein 10

Proofreading exoribonuclease

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