SMTL ID : 7rdz.1

SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC - apo class

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-2-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.295, A:C.301, A:C.306, A:C.310 ZN.2: 6 residues within 4Å: Chain A: C.487, K.532, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.487, A:H.642, A:C.645, A:C.646 ZN.5: 5 residues within 4Å: Chain E: C.9, L.11, C.12, C.30, C.33 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.9, E:C.12, E:C.30, E:C.33 ZN.6: 5 residues within 4Å: Chain E: C.54, A.56, C.59, C.76, H.79 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.54, E:C.59, E:C.76, E:H.79 ZN.7: 4 residues within 4Å: Chain E: C.20, C.23, H.37, H.43 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.20, E:C.23, E:H.37, E:H.43 ZN.8: 7 residues within 4Å: Chain F: C.9, L.11, C.12, S.14, C.30, C.33, V.102 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.9, F:C.12, F:C.30, F:C.33 ZN.9: 6 residues within 4Å: Chain F: C.54, A.56, C.59, V.61, C.76, H.79 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.54, F:C.59, F:C.76, F:H.79 ZN.10: 6 residues within 4Å: Chain F: C.20, A.22, C.23, H.37, T.41, H.43 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.20, F:C.23, F:H.37, F:H.43

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: N.209, D.218 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.218

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 15 residues within 4Å: Chain A: F.35, K.50, N.52, K.73, R.74, H.75, N.79, R.116, D.208, N.209, Y.217, D.218, G.220, D.221 Ligands: MG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.52, A:K.73, A:H.75, A:N.79, A:Y.217 Salt bridges: A:K.50, A:K.73, A:K.73, A:R.116 pi-Stacking: A:H.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, J. et al., Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex. Nat.Struct.Mol.Biol. (2022)

Release Date

2021-11-24

Peptides

RNA-directed RNA polymerase: A
Non-structural protein 8: BD
Non-structural protein 7: C
Helicase: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

E
E

F
F

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

Helicase

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