SMTL ID : 7egq.1

Co-transcriptional capping machineries in SARS-CoV-2 RTC: Coupling of N7-methyltransferase and 3'-5' exoribonuclease with polymerase reveals mechanisms for capping and proofreading

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

26 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.16, C.19, H.33, H.39, F.106 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.16, E:C.19, E:H.33, E:H.39 ZN.4: 6 residues within 4Å: Chain E: C.5, C.8, C.26, C.29, G.99, S.100 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, C.55, V.57, 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 G: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.74, G:C.77, G:H.83, G:C.90 ZN.7: 4 residues within 4Å: Chain G: C.117, V.119, C.120, C.130 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.117, G:C.120, G:C.130 ZN.8: 4 residues within 4Å: Chain H: C.207, C.210, C.226, H.229 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.207, H:C.210, H:C.226, H:H.229 ZN.9: 4 residues within 4Å: Chain H: H.257, C.261, H.264, C.279 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:H.257, H:H.257, H:C.261, H:H.264, H:C.279 ZN.10: 5 residues within 4Å: Chain H: P.451, C.452, C.477, C.484, H.487 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.452, H:C.484, H:H.487, H:H.487 ZN.13: 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.14: 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.15: 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.16: 4 residues within 4Å: Chain M: C.5, C.8, 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.17: 4 residues within 4Å: Chain M: C.50, C.55, C.72, 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.18: 4 residues within 4Å: Chain O: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.74, O:C.77, O:H.83, O:C.90 ZN.19: 4 residues within 4Å: Chain O: C.117, V.119, C.120, C.130 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:C.117, O:C.120, O:C.130 ZN.20: 5 residues within 4Å: Chain P: C.207, C.210, R.212, C.226, H.229 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.207, P:C.210, P:C.226, P:H.229 ZN.21: 4 residues within 4Å: Chain P: H.257, C.261, H.264, C.279 5 PLIP interactions: 5 interactions with chain P Metal complexes: P:H.257, P:H.257, P:C.261, P:H.264, P:C.279 ZN.22: 6 residues within 4Å: Chain P: P.451, C.452, E.453, C.477, C.484, H.487 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:C.452, P:C.484, P:H.487 ZN.24: 5 residues within 4Å: Chain Q: C.5, C.8, C.26, C.29, G.99 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.5, Q:C.8, Q:C.26, Q:C.29 ZN.25: 5 residues within 4Å: Chain Q: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.50, Q:C.55, Q:C.72, Q:H.75 ZN.26: 4 residues within 4Å: Chain Q: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.16, Q:C.19, Q:H.33, Q:H.39 ZN.27: 5 residues within 4Å: Chain R: C.5, C.8, C.26, C.29, G.99 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.5, R:C.8, R:C.26, R:C.29 ZN.28: 5 residues within 4Å: Chain R: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.50, R:C.55, R:C.72, R:H.75 ZN.29: 4 residues within 4Å: Chain R: C.16, C.19, H.33, H.39 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:C.16, R:C.19, R:H.33, R:H.33, R:H.39

3 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 3 residues within 4Å: Chain H: D.90, E.92, D.273 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.90, H:D.273 MG.12: 4 residues within 4Å: Chain H: N.266, H.268, V.269, C.272 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:V.269 MG.23: 4 residues within 4Å: Chain P: D.90, V.91, E.92, D.273 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.90, P:E.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L. et al., Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading. Cell (2021)

Release Date

2021-07-21

Peptides

RNA-directed RNA polymerase: AI
Non-structural protein 8: BDJL
Non-structural protein 7: CK
Helicase: EMQR
Non-structural protein 9: FN
Non-structural protein 10: GO
Proofreading exoribonuclease: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

I
N

B
B

D
D

J
O

L
Q

C
C

K
P

E
E

M
R

Q
F

R
S

F
G

N
T

G
H

O
U

H
K

P
X

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

Helicase

Non-structural protein 9

Non-structural protein 10

Proofreading exoribonuclease

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