SMTL ID : 8xch.1

SARS-CoV-2 Replication-Transcription Complex has a dimer-of-dimeric architecture (ddRTC) in pre-capping initiation.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-4-8-4-8-mer

Ligands

32 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.3: 5 residues within 4Å: Chain E: C.5, C.8, S.10, 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.4: 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.5: 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.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 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.10: 4 residues within 4Å: Chain I: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.295, I:C.301, I:C.306, I:C.310 ZN.11: 5 residues within 4Å: Chain I: C.487, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.487, I:H.642, I:C.645, I:C.646 ZN.13: 4 residues within 4Å: Chain M: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.16, M:C.19, M:H.33, M:H.39 ZN.14: 5 residues within 4Å: Chain M: C.5, C.8, S.10, C.26, C.29 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.5, M:C.8, M:C.26, M:C.29 ZN.15: 6 residues within 4Å: Chain M: C.50, A.52, C.55, C.72, S.74, H.75 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.50, M:C.55, M:C.72, M:H.75 ZN.16: 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.17: 4 residues within 4Å: Chain N: C.50, 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.18: 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.19: 4 residues within 4Å: Chain Q: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:H.295, Q:C.301, Q:C.306, Q:C.310 ZN.20: 5 residues within 4Å: Chain Q: C.487, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.487, Q:H.642, Q:C.645, Q:C.646 ZN.21: 5 residues within 4Å: Chain U: C.5, C.8, S.10, C.26, C.29 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.5, U:C.8, U:C.26, U:C.29 ZN.22: 4 residues within 4Å: Chain U: C.50, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.50, U:C.55, U:C.72, U:H.75 ZN.23: 4 residues within 4Å: Chain U: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:C.16, U:C.19, U:H.33, U:H.39 ZN.24: 4 residues within 4Å: Chain V: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.5, V:C.8, V:C.26, V:C.29 ZN.25: 5 residues within 4Å: Chain V: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.50, V:C.55, V:C.72, V:H.75 ZN.26: 4 residues within 4Å: Chain V: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.16, V:C.19, V:H.33, V:H.39 ZN.27: 4 residues within 4Å: Chain Y: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:H.295, Y:C.301, Y:C.306, Y:C.310 ZN.28: 5 residues within 4Å: Chain Y: C.487, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.487, Y:H.642, Y:C.645, Y:C.646 ZN.30: 4 residues within 4Å: Chain 2: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.16, 2:C.19, 2:H.33, 2:H.39 ZN.31: 5 residues within 4Å: Chain 2: C.5, C.8, S.10, C.26, C.29 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.5, 2:C.8, 2:C.26, 2:C.29 ZN.32: 6 residues within 4Å: Chain 2: C.50, A.52, C.55, C.72, S.74, H.75 4 PLIP interactions: 4 interactions with chain 2 Metal complexes: 2:C.50, 2:C.55, 2:C.72, 2:H.75 ZN.33: 4 residues within 4Å: Chain 3: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain 3 Metal complexes: 3:C.5, 3:C.8, 3:C.26, 3:C.29 ZN.34: 5 residues within 4Å: Chain 3: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain 3 Metal complexes: 3:C.50, 3:C.55, 3:C.72, 3:H.75 ZN.35: 4 residues within 4Å: Chain 3: C.16, C.19, H.33, H.39 5 PLIP interactions: 5 interactions with chain 3 Metal complexes: 3:C.16, 3:C.19, 3:H.33, 3:H.39, 3:H.39

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

ADP.6: 12 residues within 4Å: Chain E: P.284, G.285, T.286, G.287, K.288, S.289, H.290, K.320, R.442, R.443, E.540, R.567 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.285, E:G.287, E:K.288, E:S.289, E:H.290, E:R.442, E:R.443, E:E.540, E:R.567 Salt bridges: E:K.288, E:R.443, E:R.443 pi-Cation interactions: E:H.290, E:H.290 ADP.36: 11 residues within 4Å: Chain 3: E.261, G.285, T.286, K.288, S.289, H.290, K.320, R.442, R.443, E.540 Ligands: PO4.37 12 PLIP interactions: 12 interactions with chain 3 Hydrogen bonds: 3:E.261, 3:G.285, 3:K.288, 3:S.289, 3:R.442, 3:R.442, 3:R.443, 3:E.540 Salt bridges: 3:K.288, 3:K.320, 3:K.320 pi-Stacking: 3:H.290

2 x MG: MAGNESIUM ION(Non-covalent)

MG.12: 4 residues within 4Å: Chain I: D.208, N.209, Q.210, Y.217 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:D.208, I:N.209, I:Y.217 MG.29: 4 residues within 4Å: Chain Y: D.208, N.209, Q.210, Y.217 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:N.209

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.37: 8 residues within 4Å: Chain 3: K.288, E.375, R.443, Q.537, G.538, S.539, R.567 Ligands: ADP.36 5 PLIP interactions: 5 interactions with chain 3 Hydrogen bonds: 3:E.375, 3:S.539 Salt bridges: 3:K.288, 3:R.443, 3:R.567

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L. et al., Structural basis for template-product RNA duplex unwinding by SARS-CoV-2 helicase. To Be Published

Release Date

2025-06-11

Peptides

Replicase polyprotein 1ab: AIQY
Non-structural protein 8: BDJLRTZ1
Non-structural protein 7: CKS0
Helicase: EFMNUV23

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

I
I

Q
Q

Y
Y

B
B

D
D

J
J

L
L

R
R

T
T

Z
Z

1
b

C
C

K
K

S
S

0
a

E
E

F
F

M
M

N
N

U
U

V
V

2
c

3
d

Replicase polyprotein 1ab

Non-structural protein 8

Non-structural protein 7

Helicase

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