SMTL ID : 9imk.1

SARS-CoV-2 Replication-Transcription Complex has a dimer architecture (dRTC) in post-capping state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.01 Å

Oligo State

hetero-2-4-2-4-2-mer

Ligands

16 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, K.532, 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.3: 4 residues within 4Å: Chain E: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.16, E:C.19, E:H.33, E:H.39 ZN.4: 4 residues within 4Å: Chain E: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.5, E:C.8, E:C.26, E:C.29 ZN.5: 5 residues within 4Å: Chain E: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.50, E:C.55, E:C.72, E:H.75 ZN.6: 4 residues within 4Å: Chain F: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.16, F:C.19, F:H.33, F:H.39 ZN.7: 4 residues within 4Å: Chain F: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.5, F:C.8, F:C.26, F:C.29 ZN.8: 5 residues within 4Å: Chain F: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.50, F:C.55, F:C.72, F:H.75 ZN.9: 4 residues within 4Å: Chain J: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.295, J:C.301, J:C.306, J:C.310 ZN.10: 5 residues within 4Å: Chain J: C.487, K.532, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.487, J:H.642, J:C.645, J:C.646 ZN.11: 4 residues within 4Å: Chain N: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.16, N:C.19, N:H.33, N:H.39 ZN.12: 4 residues within 4Å: Chain N: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.5, N:C.8, N:C.26, N:C.29 ZN.13: 5 residues within 4Å: Chain N: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.50, N:C.55, N:C.72, N:H.75 ZN.14: 4 residues within 4Å: Chain O: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.16, O:C.19, O:H.33, O:H.39 ZN.15: 4 residues within 4Å: Chain O: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.5, O:C.8, O:C.26, O:C.29 ZN.16: 5 residues within 4Å: Chain O: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.50, O:C.55, O:C.72, O:H.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L.M. et al., Structural basis for concurrence of template recycling and RNA capping in SARS-CoV-2 replication/transcription. To Be Published

Release Date

2025-08-20

Peptides

RNA-directed RNA polymerase nsp12: AJ
Non-structural protein 8: BDKM
Non-structural protein 7: CL
Helicase nsp13: EFNO
Viral protein genome-linked nsp9: GP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

J
H

B
B

D
D

K
I

M
K

C
C

L
J

E
E

F
F

N
L

O
M

G
G

P
N

RNA-directed RNA polymerase nsp12

Non-structural protein 8

Non-structural protein 7

Helicase nsp13

Viral protein genome-linked nsp9

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