SMTL ID : 9imm.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.22 Å

Oligo State

hetero-1-2-1-2-1-mer

Ligands

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

A-A-C-C-U-U-C-C-C.1: 8 residues within 4Å: Chain A: S.78 Chain H: A.4, A.5, A.6, G.7, G.8, U.9, U.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.52, A:N.52, A:N.52 Salt bridges: A:K.73

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 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.4: 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.5: 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.6: 4 residues within 4Å: Chain E: C.50, 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.7: 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.8: 5 residues within 4Å: Chain F: C.5, L.7, 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.9: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2025-08-20

Peptides

RNA-directed RNA polymerase nsp12: A
Non-structural protein 8: BD
Non-structural protein 7: C
Helicase nsp13: EF
Viral protein genome-linked nsp9: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

E
E

F
F

G
G

RNA-directed RNA polymerase nsp12

Non-structural protein 8

Non-structural protein 7

Helicase nsp13

Viral protein genome-linked nsp9

Related Entries With Identical Sequence