SMTL ID : 8aov.1

CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with GTP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:E.129, A:C.134, A:C.141 ZN.3: 4 residues within 4Å: Chain B: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.79, B:E.129, B:C.134, B:C.141 ZN.5: 4 residues within 4Å: Chain C: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.79, C:E.129, C:C.134, C:C.141 ZN.7: 4 residues within 4Å: Chain D: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.79, D:E.129, D:C.134, D:C.141 ZN.9: 4 residues within 4Å: Chain E: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.79, E:E.129, E:C.134, E:C.141 ZN.11: 4 residues within 4Å: Chain F: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.79, F:E.129, F:C.134, F:C.141 ZN.13: 4 residues within 4Å: Chain G: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.79, G:E.129, G:C.134, G:C.141 ZN.15: 4 residues within 4Å: Chain H: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.79, H:E.129, H:C.134, H:C.141 ZN.17: 4 residues within 4Å: Chain I: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.79, I:E.129, I:C.134, I:C.141 ZN.19: 4 residues within 4Å: Chain J: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.79, J:E.129, J:C.134, J:C.141 ZN.21: 4 residues within 4Å: Chain K: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.79, K:E.129, K:C.134, K:C.141 ZN.23: 4 residues within 4Å: Chain L: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:H.79, L:E.129, L:C.134, L:C.141

12 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.2: 12 residues within 4Å: Chain A: H.37, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.70, A:D.152, A:Y.248, A:Y.285 Salt bridges: A:H.37, A:R.41, A:R.41, A:E.250 pi-Stacking: A:Y.248, A:Y.248 GTP.4: 12 residues within 4Å: Chain B: H.37, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.37, B:R.70, B:Y.248, B:Y.285 Salt bridges: B:H.37, B:R.41, B:R.41, B:E.250 pi-Stacking: B:Y.248, B:Y.248 GTP.6: 12 residues within 4Å: Chain C: H.37, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.44, C:S.44, C:R.70, C:Y.248, C:Y.285 Salt bridges: C:H.37, C:R.41, C:R.41, C:E.250 pi-Stacking: C:Y.248, C:Y.248 GTP.8: 12 residues within 4Å: Chain D: H.37, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.44, D:S.44, D:R.70, D:Y.248, D:Y.285 Salt bridges: D:H.37, D:R.41, D:R.41, D:E.250 pi-Stacking: D:Y.248, D:Y.248 GTP.10: 11 residues within 4Å: Chain E: H.37, A.40, R.41, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:H.37, E:D.152, E:Y.248, E:E.250, E:E.250, E:Y.285 Salt bridges: E:H.37, E:R.41, E:R.41 pi-Stacking: E:Y.248, E:Y.248 GTP.12: 12 residues within 4Å: Chain F: H.37, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.44, F:S.44, F:R.70, F:Y.248, F:Y.285 Salt bridges: F:H.37, F:R.41, F:R.41, F:E.250 pi-Stacking: F:Y.248, F:Y.248 GTP.14: 11 residues within 4Å: Chain G: H.37, A.40, R.41, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:S.44, G:S.44, G:Y.248, G:Y.285 Salt bridges: G:H.37, G:R.41, G:R.41, G:E.250 pi-Stacking: G:Y.248, G:Y.248 GTP.16: 11 residues within 4Å: Chain H: H.37, R.41, R.70, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:S.44, H:S.44, H:R.70, H:Y.248, H:Y.285 Salt bridges: H:H.37, H:R.41, H:R.41, H:E.250 pi-Stacking: H:Y.248, H:Y.248 GTP.18: 12 residues within 4Å: Chain I: H.37, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:R.70, I:Y.248, I:Y.285 Salt bridges: I:H.37, I:R.41, I:R.41, I:E.250 pi-Stacking: I:Y.248, I:Y.248 GTP.20: 12 residues within 4Å: Chain J: H.37, A.40, R.41, S.44, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:S.44, J:S.44, J:Y.248, J:Y.285 Salt bridges: J:H.37, J:R.41, J:R.41, J:E.250 pi-Stacking: J:Y.248, J:Y.248 GTP.22: 12 residues within 4Å: Chain K: H.37, A.40, R.41, R.70, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:S.44, K:S.44, K:R.70, K:Y.248, K:Y.285 Salt bridges: K:H.37, K:R.41, K:R.41, K:E.250 pi-Stacking: K:Y.248, K:Y.248 GTP.24: 11 residues within 4Å: Chain L: H.37, A.40, R.41, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:S.44, L:S.44, L:Y.248, L:Y.285 Salt bridges: L:H.37, L:R.41, L:R.41, L:E.250 pi-Stacking: L:Y.248, L:Y.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, R. et al., Structural basis and dynamics of Chikungunya alphavirus RNA capping by nsP1 capping pores. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-05-31

Peptides

mRNA-capping enzyme nsP1: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

E
I

F
K

G
M

H
O

I
Q

J
S

K
V

L
X

mRNA-capping enzyme nsP1

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