SMTL ID : 9ikz.1

SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3-

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.14 Å

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: 4 residues within 4Å: Chain A: C.487, H.642, C.645, C.646 No protein-ligand interaction detected (PLIP) ZN.6: 6 residues within 4Å: Chain E: C.16, G.17, A.18, C.19, H.33, H.39 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.16, E:H.33, E:H.39 ZN.7: 5 residues within 4Å: Chain E: C.5, C.8, C.26, C.29, G.99 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:C.8 ZN.8: 5 residues within 4Å: Chain E: C.50, A.52, C.55, V.57, S.74 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:C.55, E:S.74 ZN.9: 5 residues within 4Å: Chain F: C.16, A.18, C.19, H.33, H.39 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.19, F:H.33 ZN.10: 4 residues within 4Å: Chain F: C.5, C.8, C.26, C.29 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.5, F:C.8 ZN.11: 2 residues within 4Å: Chain F: A.52, C.72 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:C.72

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

GDP.3: 22 residues within 4Å: Chain A: R.33, F.35, K.50, N.52, C.53, R.55, Y.69, V.71, K.73, R.116, T.120, K.121, Y.122, T.123, D.208, N.209, D.211, Y.217, D.218 Chain G: N.1 Ligands: BEF.4, MG.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.52, A:N.52, A:R.55, A:T.120, A:D.208, A:D.208, A:Y.217, A:Y.217 Salt bridges: A:K.50, A:K.50, A:K.73, A:K.73, A:R.116 pi-Cation interactions: A:R.33

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.4: 5 residues within 4Å: Chain A: K.73, D.218 Chain G: N.1 Ligands: GDP.3, MG.5 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.208, N.209, D.218 Ligands: GDP.3, BEF.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Y.C. et al., Substrate selection and transition reveal the mechanism for RNA capping catalyzed by SARS-CoV-2 NiRAN. To Be Published

Release Date

2025-06-18

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

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