SMTL ID : 7y38.1

Molecular architecture of the chikungunya virus replication complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-1-1-mer

Ligands

1 x C- C- A: RNA (5'-R(P*CP*CP*A)-3')(Non-covalent)

C-C-A.1: 8 residues within 4Å: Chain N: Y.161, F.164, K.210, K.211, D.235, S.236, N.240, F.287 Protein-ligand interaction information (PLIP) not available

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.5: 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.8: 4 residues within 4Å: Chain C: H.79, E.129, C.134, C.141 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.79, C:C.134, C:C.141 ZN.11: 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.14: 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.17: 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.20: 4 residues within 4Å: Chain G: H.79, E.129, C.134, C.141 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.79, G:C.134, G:C.141 ZN.23: 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.26: 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.29: 4 residues within 4Å: Chain J: H.79, E.129, C.134, C.141 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:H.79, J:C.134, J:C.141 ZN.32: 4 residues within 4Å: Chain K: H.79, E.129, C.134, C.141 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:H.79, K:C.134, K:C.141 ZN.35: 4 residues within 4Å: Chain L: H.79, E.129, C.134, C.141 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:H.79, L:C.134, L:C.141

12 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 9 residues within 4Å: Chain A: P.83, R.85, S.86, D.89, D.138, A.155, P.249, E.250 Ligands: GTP.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.85, A:D.89, A:D.138, A:D.138, A:P.249, A:P.249 ATP.7: 8 residues within 4Å: Chain B: P.83, S.86, D.89, D.138, A.155, P.249, E.250 Ligands: GTP.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.85, B:D.89, B:D.138, B:D.138, B:E.250 ATP.10: 11 residues within 4Å: Chain C: I.64, G.65, P.83, R.85, S.86, D.89, D.138, A.155, P.249, E.250 Ligands: GTP.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:P.83, C:R.92, C:D.138, C:D.138, C:P.249, C:E.250 ATP.13: 12 residues within 4Å: Chain C: K.299 Chain D: I.64, P.83, R.85, S.86, D.89, D.138, A.155, Y.248, P.249, E.250 Ligands: GTP.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.89, D:R.92, D:D.138, D:D.138, D:E.250 ATP.16: 10 residues within 4Å: Chain E: P.83, R.85, S.86, D.89, R.92, D.138, A.155, P.249, E.250 Ligands: GTP.15 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:D.89, E:R.92, E:D.138, E:D.138, E:E.250, E:E.250 ATP.19: 12 residues within 4Å: Chain F: I.64, G.65, P.83, R.85, S.86, D.89, T.137, D.138, A.155, P.249, E.250 Ligands: GTP.18 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:P.83, F:R.92, F:D.138, F:D.138, F:P.249, F:E.250 ATP.21: 12 residues within 4Å: Chain G: I.64, P.83, R.85, S.86, D.89, R.92, D.138, A.155, Y.248, P.249, E.250 Ligands: GTP.22 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:R.85, G:D.89, G:R.92, G:D.138, G:D.138 ATP.24: 10 residues within 4Å: Chain H: I.64, P.83, R.85, S.86, D.89, D.138, A.155, Y.248, P.249, E.250 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:D.89, H:D.138, H:D.138 ATP.27: 10 residues within 4Å: Chain I: I.64, G.65, P.83, R.85, S.86, D.89, R.92, D.138, A.155, P.249 7 PLIP interactions: 7 interactions with chain I Hydrogen bonds: I:R.85, I:S.86, I:S.86, I:D.89, I:R.92, I:D.138, I:D.138 ATP.31: 11 residues within 4Å: Chain J: I.64, P.83, R.85, S.86, D.89, T.137, D.138, A.155, P.249, E.250 Ligands: GTP.30 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:R.85, J:D.89, J:D.138, J:D.138, J:P.249, J:E.250 ATP.33: 11 residues within 4Å: Chain K: G.65, P.83, R.85, S.86, D.89, T.137, D.138, A.155, P.249, E.250 Ligands: GTP.34 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:D.89, K:D.138, K:D.138, K:P.249, K:P.249 ATP.36: 12 residues within 4Å: Chain L: G.65, P.83, R.85, S.86, D.89, T.137, D.138, A.155, Y.248, P.249, E.250 Ligands: GTP.37 6 PLIP interactions: 6 interactions with chain L Hydrogen bonds: L:P.83, L:D.89, L:D.138, L:D.138, L:E.250, L:E.250

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

GTP.4: 12 residues within 4Å: Chain A: A.40, R.41, E.88, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: ATP.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.40, A:R.41, A:E.88, A:Y.285 Salt bridges: A:R.41, A:R.92, A:E.250 pi-Stacking: A:Y.248, A:Y.248 pi-Cation interactions: A:Y.248 GTP.6: 12 residues within 4Å: Chain A: D.277 Chain B: A.40, R.41, R.92, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285 Ligands: ATP.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.44, B:R.92, B:T.246, B:Y.248, B:Y.285, B:Y.285 Salt bridges: B:E.250 pi-Stacking: B:Y.248, B:Y.248 pi-Cation interactions: B:Y.248 GTP.9: 10 residues within 4Å: Chain C: R.41, E.88, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250 Ligands: ATP.10 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.152, C:Y.248 Salt bridges: C:R.41, C:R.92, C:E.250 pi-Stacking: C:Y.248, C:Y.248 GTP.12: 10 residues within 4Å: Chain D: A.40, R.41, R.70, R.92, D.152, Y.154, F.241, Y.248, E.250 Ligands: ATP.13 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.70, D:D.152, D:Y.248, D:Y.248 Salt bridges: D:R.41, D:R.92, D:E.250 pi-Stacking: D:Y.248 pi-Cation interactions: D:Y.248 GTP.15: 11 residues within 4Å: Chain E: N.35, A.40, R.41, R.92, D.152, Y.154, V.243, Y.248, E.250, Y.285 Ligands: ATP.16 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:N.35, E:A.40, E:R.92, E:Y.248, E:Y.248, E:Y.285 Salt bridges: E:R.41, E:E.250 pi-Stacking: E:Y.248, E:Y.248 pi-Cation interactions: E:Y.248 GTP.18: 9 residues within 4Å: Chain F: A.40, R.41, R.92, D.152, Y.154, Y.248, E.250, Y.285 Ligands: ATP.19 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:D.152, F:Y.285 Salt bridges: F:R.41, F:R.92, F:E.250 pi-Stacking: F:Y.248, F:Y.248 pi-Cation interactions: F:Y.248 GTP.22: 10 residues within 4Å: Chain G: A.40, R.41, R.70, D.152, Y.154, T.246, Y.248, E.250, Y.285 Ligands: ATP.21 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:R.41, G:R.70, G:D.152, G:T.246, G:Y.248 Salt bridges: G:R.41, G:E.250 pi-Stacking: G:Y.248 pi-Cation interactions: G:Y.248 GTP.25: 6 residues within 4Å: Chain H: A.40, R.41, D.152, Y.154, Y.248, E.250 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:Y.248, H:Y.248 Salt bridges: H:R.41, H:E.250 pi-Stacking: H:Y.248 pi-Cation interactions: H:Y.248 GTP.28: 9 residues within 4Å: Chain I: R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:R.70, I:R.92, I:R.92, I:Y.248 Salt bridges: I:R.41, I:E.250 pi-Stacking: I:Y.248, I:Y.248 pi-Cation interactions: I:Y.248 GTP.30: 10 residues within 4Å: Chain J: A.40, R.41, R.70, R.92, D.152, Y.154, T.246, Y.248, E.250 Ligands: ATP.31 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:R.41, J:R.70, J:R.92, J:D.152, J:T.246, J:Y.248 Salt bridges: J:R.41, J:E.250 pi-Stacking: J:Y.248, J:Y.248 pi-Cation interactions: J:Y.248 GTP.34: 11 residues within 4Å: Chain K: A.40, R.41, E.88, R.92, D.152, Y.154, F.241, Y.248, E.250, Y.285 Ligands: ATP.33 9 PLIP interactions: 9 interactions with chain K Hydrogen bonds: K:R.41, K:E.88, K:D.152, K:Y.248, K:Y.285 Salt bridges: K:R.92, K:E.250 pi-Stacking: K:Y.248, K:Y.248 GTP.37: 10 residues within 4Å: Chain K: R.275 Chain L: R.41, R.92, D.152, Y.154, F.241, Y.248, E.250, Y.285 Ligands: ATP.36 10 PLIP interactions: 9 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:D.152, L:Y.248, L:Y.248, L:Y.285, K:R.275 Salt bridges: L:R.92, L:E.250 pi-Stacking: L:Y.248, L:Y.248 pi-Cation interactions: L:Y.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, Y.B. et al., Molecular architecture of the Chikungunya virus replication complex. Sci Adv (2022)

Release Date

2022-12-14

Peptides

mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG): ABCDEFGHIJKL
RNA-directed RNA polymerase nsP4: M
Protease nsP2: N

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

M
X

N
Y

mRNA-capping enzyme nsP1,affinity-tag (strepII-3XFLAG)

RNA-directed RNA polymerase nsP4

Protease nsP2