SMTL ID : 7cyq.1

Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex reveals an intermediate state in cap synthesis

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-2-1-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: 5 residues within 4Å: Chain A: C.487, 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 G: C.16, C.19, H.33, H.39, A.110 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.16, G:C.19, G:H.33, G:H.39 ZN.6: 4 residues within 4Å: Chain G: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.5, G:C.8, G:C.26, G:C.29 ZN.7: 5 residues within 4Å: Chain G: C.50, C.55, V.57, C.72, H.75 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.50, G:C.55, G:C.72, G:H.75 ZN.8: 5 residues within 4Å: Chain H: C.16, C.19, H.33, H.39, A.110 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.16, H:C.19, H:H.33, H:H.39 ZN.9: 4 residues within 4Å: Chain H: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.5, H:C.8, H:C.26, H:C.29 ZN.10: 5 residues within 4Å: Chain H: C.50, C.55, V.57, C.72, H.75 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.50, H:C.55, H:C.72, H:H.75

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 10 residues within 4Å: Chain A: K.50, N.52, K.73, H.75, R.116, N.209, Y.217, D.218 Chain I: N.5 Ligands: MG.4 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain I Salt bridges: A:K.50, A:K.73, A:K.73, A:R.116 pi-Stacking: A:H.75 Hydrogen bonds: I:N.5, I:N.5, I:N.5

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.208, N.209, D.218 Chain I: N.5 Ligands: GDP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L. et al., Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis. Cell (2021)

Release Date

2020-12-09

Peptides

RNA-directed RNA polymerase: A
Non-structural protein 8: BD
Non-structural protein 7: C
Helicase: GH
Non-structural protein 9: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

G
F

H
E

I
G

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

Helicase

Non-structural protein 9

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