SMTL ID : 8apx.1

CryoEM structure of the Chikungunya virus nsP1 capping pores in covalent complex with a 7GMP cap structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.79, V.81, 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: 5 residues within 4Å: Chain B: H.79, V.81, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.79, B:H.79, B:E.129, B:C.134, B:C.141 ZN.5: 5 residues within 4Å: Chain C: H.79, V.81, 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 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.79, D:H.79, D:E.129, D:C.134, D:C.141 ZN.9: 5 residues within 4Å: Chain E: H.79, V.81, 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: 5 residues within 4Å: Chain F: H.79, V.81, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:H.79, F:H.79, F:E.129, F:C.134, F:C.141 ZN.13: 5 residues within 4Å: Chain G: H.79, V.81, 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: 5 residues within 4Å: Chain H: H.79, V.81, 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: 5 residues within 4Å: Chain I: H.79, V.81, 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: 5 residues within 4Å: Chain J: H.79, V.81, 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 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:H.79, K:H.79, K:E.129, K:C.134, K:C.141 ZN.23: 5 residues within 4Å: Chain L: H.79, V.81, 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 SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 16 residues within 4Å: Chain A: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, E.88, D.89, T.137, D.138, Q.151, D.152, A.155, V.156 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.65, A:G.65, A:R.85, A:S.86, A:E.88, A:D.89, A:D.138, A:D.138, A:Q.151 Salt bridges: A:R.41, A:R.70 SAH.4: 13 residues within 4Å: Chain B: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, D.89, D.138, Q.151, D.152, A.155 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.65, B:G.65, B:R.85, B:S.86, B:D.89, B:D.138, B:D.138, B:Q.151 Salt bridges: B:R.41, B:R.70 SAH.6: 14 residues within 4Å: Chain C: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, D.89, D.138, Q.151, D.152, A.155, V.156 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.65, C:G.65, C:R.85, C:S.86, C:S.86, C:D.89, C:D.138, C:D.138, C:Q.151 Salt bridges: C:R.41, C:R.70 SAH.8: 15 residues within 4Å: Chain D: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, E.88, D.89, T.137, D.138, Q.151, D.152, A.155 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.65, D:G.65, D:R.85, D:S.86, D:D.89, D:D.138, D:Q.151 Salt bridges: D:R.41, D:R.70 SAH.10: 15 residues within 4Å: Chain E: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, D.89, T.137, D.138, Q.151, D.152, A.155, V.156 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.65, E:G.65, E:R.85, E:S.86, E:S.86, E:D.138, E:D.138, E:Q.151 Salt bridges: E:R.41, E:R.70 SAH.12: 16 residues within 4Å: Chain F: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, E.88, D.89, T.137, D.138, Q.151, D.152, A.155, V.156 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.65, F:G.65, F:R.85, F:S.86, F:S.86, F:D.89, F:D.138, F:D.138, F:Q.151 Salt bridges: F:R.41, F:R.70 SAH.14: 15 residues within 4Å: Chain G: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, E.88, D.89, T.137, D.138, Q.151, D.152, A.155 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:G.65, G:G.65, G:R.85, G:S.86, G:D.89, G:T.137, G:T.137, G:D.138, G:Q.151 Salt bridges: G:R.41, G:R.70 SAH.16: 14 residues within 4Å: Chain H: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, D.89, T.137, D.138, Q.151, D.152, A.155 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:G.65, H:G.65, H:R.85, H:S.86, H:D.89, H:T.137, H:D.138, H:D.138, H:Q.151 Salt bridges: H:R.41, H:R.70 SAH.18: 13 residues within 4Å: Chain I: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, D.89, D.138, Q.151, D.152, A.155 11 PLIP interactions: 11 interactions with chain I Hydrogen bonds: I:G.65, I:G.65, I:R.85, I:S.86, I:S.86, I:D.89, I:D.138, I:D.138, I:Q.151 Salt bridges: I:R.41, I:R.70 SAH.20: 15 residues within 4Å: Chain J: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, E.88, D.89, T.137, D.138, Q.151, D.152, A.155 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:G.65, J:G.65, J:R.85, J:S.86, J:E.88, J:D.89, J:D.138, J:Q.151 Salt bridges: J:R.41, J:R.70 SAH.22: 13 residues within 4Å: Chain K: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, D.89, D.138, Q.151, D.152, A.155 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:G.65, K:G.65, K:R.85, K:S.86, K:D.89, K:D.138, K:D.138, K:Q.151 Salt bridges: K:R.41, K:R.70 SAH.24: 13 residues within 4Å: Chain L: X.37, R.41, I.64, G.65, R.70, P.83, R.85, S.86, D.89, D.138, Q.151, D.152, A.155 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:G.65, L:G.65, L:R.85, L:S.86, L:D.89, L:D.138, L:D.138, L:Q.151 Salt bridges: L:R.41, L:R.70

Links

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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

2023-05-03

Peptides

Polyprotein P1234: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Polyprotein P1234