SMTL ID : 7n0d.1

Cryo-EM structure of the tetrameric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

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

C-C-C-C-C.1: 22 residues within 4Å: Chain B: R.98 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, H.268 Chain E: G.1, G.2, G.3, G.4, A.5 Ligands: MG.12 13 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C, 6 interactions with chain D Hydrogen bonds: B:K.13, B:H.95, B:N.104, B:N.104, B:N.104, C:A.1, D:G.102, D:N.104, D:N.104, D:N.104 Salt bridges: B:K.13, D:K.9, D:K.9 C-C-C-C-C.2: 22 residues within 4Å: Chain H: R.98 Chain J: 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, H.268 Chain K: G.1, G.2, G.3, G.4, A.5 Ligands: MG.27 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.7: 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.8: 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.9: 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.10: 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.11: 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.13: 5 residues within 4Å: Chain D: C.207, C.208, 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.14: 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.15: 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.17: 4 residues within 4Å: Chain G: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.74, G:C.77, G:H.83, G:C.90 ZN.18: 4 residues within 4Å: Chain G: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.117, G:C.120, G:C.128, G:C.130 ZN.21: 4 residues within 4Å: Chain H: C.207, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.207, H:C.210, H:C.226, H:H.229 ZN.22: 4 residues within 4Å: Chain H: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.257, H:C.261, H:H.264, H:C.279 ZN.23: 4 residues within 4Å: Chain H: C.452, C.477, C.484, H.487 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.452, H:C.477, H:C.484, H:H.487 ZN.24: 4 residues within 4Å: Chain I: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.74, I:C.77, I:H.83, I:C.90 ZN.25: 4 residues within 4Å: Chain I: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.117, I:C.120, I:C.128, I:C.130 ZN.28: 5 residues within 4Å: Chain J: C.207, C.208, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.207, J:C.210, J:C.226, J:H.229 ZN.29: 4 residues within 4Å: Chain J: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.257, J:C.261, J:H.264, J:C.279 ZN.30: 4 residues within 4Å: Chain J: C.452, C.477, C.484, H.487 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.452, J:C.477, J:C.484, J:H.487

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain B: D.90, E.92, D.273 Chain F: C.22 Ligands: MG.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.90, B:D.90, B:E.92, B:D.273 MG.6: 3 residues within 4Å: Chain B: D.90 Chain F: C.22 Ligands: MG.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.90 MG.12: 4 residues within 4Å: Chain D: D.90, E.92, D.273 Ligands: C-C-C-C-C.1 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.90, D:D.90, D:E.92, D:D.273 MG.19: 5 residues within 4Å: Chain H: D.90, E.92, D.273 Chain L: C.22 Ligands: MG.20 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.90, H:D.90, H:E.92, H:D.273 MG.20: 4 residues within 4Å: Chain H: D.90 Chain L: C.21, C.22 Ligands: MG.19 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.90 MG.27: 4 residues within 4Å: Chain J: D.90, E.92, D.273 Ligands: C-C-C-C-C.2 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.90, J:D.90, J:E.92, J:D.273

2 x 1N7: CHAPSO(Non-covalent)

1N7.16: 9 residues within 4Å: Chain D: A.471, N.478, Y.517, W.520 Chain H: A.471, N.478, L.479, Y.517, W.520 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain H Hydrophobic interactions: D:A.471, D:Y.517, D:W.520, H:A.471, H:Y.517, H:W.520, H:W.520, H:W.520, H:W.520 Hydrogen bonds: D:N.478 1N7.26: 9 residues within 4Å: Chain B: A.471, N.478, L.479, Y.517, W.520 Chain J: A.471, N.478, Y.517, W.520 10 PLIP interactions: 4 interactions with chain J, 6 interactions with chain B Hydrophobic interactions: J:A.471, J:Y.517, J:W.520, B:A.471, B:Y.517, B:W.520, B:W.520, B:W.520, B:W.520 Hydrogen bonds: J:N.478

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Science (2021)

Release Date

2021-07-28

Peptides

Non-structural protein 10: ACGI
Proofreading exoribonuclease: BDHJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

G
E

I
G

B
B

D
D

H
F

J
H

Non-structural protein 10

Proofreading exoribonuclease

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