SMTL ID : 8aox.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-24-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.79, E.129, C.134, C.141, Q.143 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 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.79, B:E.129, B:C.134, B:C.141 ZN.5: 5 residues within 4Å: Chain C: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.79, C:E.129, C:C.134, C:C.141 ZN.7: 5 residues within 4Å: Chain D: H.79, V.81, 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: 5 residues within 4Å: Chain E: H.79, E.129, C.134, C.141, Q.143 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, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.79, F:E.129, F:C.134, F:C.141 ZN.13: 5 residues within 4Å: Chain G: H.79, E.129, C.134, C.141, Q.143 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, E.129, C.134, C.141, Q.143 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: 5 residues within 4Å: Chain J: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.79, J:E.129, J:C.134, J:C.141 ZN.21: 5 residues within 4Å: Chain K: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.79, K:E.129, K:C.134, K:C.141 ZN.23: 5 residues within 4Å: Chain L: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:H.79, L:E.129, L:C.134, L:C.141 ZN.25: 4 residues within 4Å: Chain M: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:H.79, M:E.129, M:C.134, M:C.141 ZN.27: 5 residues within 4Å: Chain N: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:H.79, N:E.129, N:C.134, N:C.141 ZN.29: 4 residues within 4Å: Chain O: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:H.79, O:E.129, O:C.134, O:C.141 ZN.31: 4 residues within 4Å: Chain P: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:H.79, P:E.129, P:C.134, P:C.141 ZN.33: 5 residues within 4Å: Chain Q: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:H.79, Q:E.129, Q:C.134, Q:C.141 ZN.35: 4 residues within 4Å: Chain R: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:H.79, R:E.129, R:C.134, R:C.141 ZN.37: 5 residues within 4Å: Chain S: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:H.79, S:E.129, S:C.134, S:C.141 ZN.39: 4 residues within 4Å: Chain T: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:H.79, T:E.129, T:C.134, T:C.141 ZN.41: 5 residues within 4Å: Chain U: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain U Metal complexes: U:H.79, U:E.129, U:C.134, U:C.141 ZN.43: 5 residues within 4Å: Chain V: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:H.79, V:E.129, V:C.134, V:C.141 ZN.45: 5 residues within 4Å: Chain W: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:H.79, W:E.129, W:C.134, W:C.141 ZN.47: 5 residues within 4Å: Chain X: H.79, E.129, C.134, C.141, Q.143 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:H.79, X:E.129, X:C.134, X:C.141

24 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 15 residues within 4Å: Chain A: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.67, A:R.85, A:S.86, A:S.86, A:D.89, A:R.92, A:T.137, A:D.138, A:Q.151, A:D.152 Water bridges: A:R.85, A:D.89, A:T.137, A:T.137, A:T.137 Salt bridges: A:R.70 SAM.4: 15 residues within 4Å: Chain B: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:A.67, B:R.85, B:S.86, B:S.86, B:D.89, B:R.92, B:T.137, B:D.138, B:Q.151 Water bridges: B:R.85, B:D.89, B:T.137, B:T.137, B:T.137 Salt bridges: B:R.70 SAM.6: 14 residues within 4Å: Chain C: I.64, G.65, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.153 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:A.67, C:S.86, C:D.89, C:R.92, C:T.137, C:D.138, C:Q.151, C:D.152 Water bridges: C:R.85, C:D.89, C:D.89, C:T.137, C:T.137, C:T.137 Salt bridges: C:R.70 SAM.8: 15 residues within 4Å: Chain D: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:A.67, D:R.85, D:S.86, D:D.89, D:R.92, D:T.137, D:D.138, D:Q.151, D:Q.151, D:D.152 Water bridges: D:R.85, D:D.89, D:T.137 Salt bridges: D:R.70 SAM.10: 15 residues within 4Å: Chain E: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:A.67, E:R.85, E:S.86, E:D.89, E:R.92, E:T.137, E:D.138, E:Q.151, E:D.152 Water bridges: E:R.85, E:D.89, E:T.137, E:T.137 Salt bridges: E:R.70, E:E.88 SAM.12: 14 residues within 4Å: Chain F: I.64, G.65, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:A.67, F:R.85, F:S.86, F:D.89, F:R.92, F:T.137, F:D.138, F:Q.151 Water bridges: F:R.85, F:D.89, F:T.137, F:T.137, F:T.137 Salt bridges: F:R.70 SAM.14: 16 residues within 4Å: Chain G: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.153, V.156 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:A.67, G:R.85, G:S.86, G:S.86, G:D.89, G:R.92, G:T.137, G:D.138, G:Q.151, G:Q.151 Water bridges: G:R.85, G:R.92, G:T.137 Salt bridges: G:R.70, G:E.88 SAM.16: 15 residues within 4Å: Chain H: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:A.67, H:R.85, H:S.86, H:D.89, H:R.92, H:T.137, H:D.138, H:Q.151, H:D.152 Water bridges: H:R.85, H:D.89 Salt bridges: H:R.70 SAM.18: 13 residues within 4Å: Chain I: I.64, G.65, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:A.67, I:S.86, I:D.89, I:R.92, I:T.137, I:D.138, I:Q.151, I:D.152 Water bridges: I:R.85, I:R.92, I:T.137, I:T.137 Salt bridges: I:R.70 SAM.20: 14 residues within 4Å: Chain J: I.64, G.65, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:A.67, J:R.85, J:S.86, J:S.86, J:D.89, J:R.92, J:T.137, J:D.138, J:Q.151, J:D.152 Water bridges: J:R.85, J:T.137, J:T.137, J:T.137 Salt bridges: J:R.70 SAM.22: 15 residues within 4Å: Chain K: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:A.67, K:R.85, K:S.86, K:S.86, K:D.89, K:R.92, K:T.137, K:D.138, K:Q.151, K:Q.151, K:D.152 Water bridges: K:D.89, K:T.137, K:T.137, K:T.137 Salt bridges: K:R.70 SAM.24: 16 residues within 4Å: Chain L: I.64, G.65, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.153, V.156, Y.248 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:G.65, L:A.67, L:R.85, L:S.86, L:S.86, L:D.89, L:R.92, L:T.137, L:D.138, L:D.152 Water bridges: L:R.85, L:D.89, L:T.137, L:T.137, L:T.137 Salt bridges: L:R.70, L:E.88 SAM.26: 15 residues within 4Å: Chain M: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 14 PLIP interactions: 14 interactions with chain M Hydrogen bonds: M:A.67, M:R.85, M:S.86, M:S.86, M:D.89, M:R.92, M:T.137, M:T.137, M:D.138, M:Q.151, M:Q.151 Water bridges: M:R.85 Salt bridges: M:R.70, M:E.88 SAM.28: 15 residues within 4Å: Chain N: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:A.67, N:R.85, N:S.86, N:S.86, N:D.89, N:R.92, N:T.137, N:T.137, N:D.138, N:Q.151 Salt bridges: N:R.70, N:E.88 SAM.30: 14 residues within 4Å: Chain O: I.64, G.65, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.153 12 PLIP interactions: 12 interactions with chain O Hydrogen bonds: O:A.67, O:R.85, O:S.86, O:S.86, O:D.89, O:R.92, O:T.137, O:T.137, O:D.138, O:Q.151 Water bridges: O:R.85 Salt bridges: O:R.70 SAM.32: 15 residues within 4Å: Chain P: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 12 PLIP interactions: 12 interactions with chain P Hydrogen bonds: P:A.67, P:R.85, P:S.86, P:S.86, P:D.89, P:R.92, P:T.137, P:T.137, P:D.138, P:Q.151 Water bridges: P:R.85 Salt bridges: P:R.70 SAM.34: 13 residues within 4Å: Chain Q: I.64, G.65, A.67, R.70, P.83, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.153 9 PLIP interactions: 9 interactions with chain Q Hydrogen bonds: Q:A.67, Q:D.89, Q:R.92, Q:T.137, Q:T.137, Q:D.138, Q:Q.151 Water bridges: Q:R.92 Salt bridges: Q:R.70 SAM.36: 15 residues within 4Å: Chain R: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 12 PLIP interactions: 12 interactions with chain R Hydrogen bonds: R:A.67, R:R.85, R:S.86, R:S.86, R:D.89, R:R.92, R:T.137, R:T.137, R:D.138, R:Q.151 Water bridges: R:R.85 Salt bridges: R:R.70 SAM.38: 15 residues within 4Å: Chain S: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 13 PLIP interactions: 13 interactions with chain S Hydrogen bonds: S:A.67, S:R.85, S:S.86, S:S.86, S:D.89, S:R.92, S:R.92, S:T.137, S:T.137, S:D.138, S:Q.151, S:Q.151 Salt bridges: S:R.70 SAM.40: 15 residues within 4Å: Chain T: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 13 PLIP interactions: 13 interactions with chain T Hydrogen bonds: T:A.67, T:R.85, T:S.86, T:S.86, T:D.89, T:R.92, T:T.137, T:T.137, T:D.138, T:Q.151, T:Q.151 Salt bridges: T:R.70, T:E.88 SAM.42: 15 residues within 4Å: Chain U: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 12 PLIP interactions: 12 interactions with chain U Hydrogen bonds: U:A.67, U:R.85, U:S.86, U:S.86, U:D.89, U:R.92, U:T.137, U:T.137, U:D.138, U:Q.151 Water bridges: U:R.85 Salt bridges: U:R.70 SAM.44: 15 residues within 4Å: Chain V: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 13 PLIP interactions: 13 interactions with chain V Hydrogen bonds: V:A.67, V:R.85, V:S.86, V:S.86, V:D.89, V:R.92, V:R.92, V:T.137, V:T.137, V:D.138, V:Q.151 Water bridges: V:R.85 Salt bridges: V:R.70 SAM.46: 14 residues within 4Å: Chain W: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152 12 PLIP interactions: 12 interactions with chain W Hydrogen bonds: W:A.67, W:R.85, W:S.86, W:S.86, W:D.89, W:R.92, W:T.137, W:T.137, W:D.138, W:Q.151 Water bridges: W:R.85 Salt bridges: W:R.70 SAM.48: 15 residues within 4Å: Chain X: I.64, G.65, S.66, A.67, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 12 PLIP interactions: 12 interactions with chain X Hydrogen bonds: X:A.67, X:R.85, X:S.86, X:S.86, X:D.89, X:R.92, X:T.137, X:T.137, X:D.138, X:Q.151 Water bridges: X:R.85 Salt bridges: X:R.70

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

2023-03-29

Peptides

mRNA-capping enzyme nsP1: ABCDEFGHIJKLMNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
JA

B
A

C
C

D
E

E
G

F
I

G
K

H
M

I
O

J
Q

K
S

L
V

M
X

N
Z

O
BA

P
DA

Q
FA

R
HA

S
LA

T
NA

U
PA

V
RA

W
TA

X
VA

mRNA-capping enzyme nsP1

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