SMTL ID : 8aow.1

CryoEM structure of the Chikungunya virus nsP1 capping pores in complex with m7GTP and SAH ligands

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.7: 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.12: 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.17: 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.22: 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.27: 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.32: 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.37: 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.42: 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.47: 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.52: 5 residues within 4Å: Chain K: H.79, V.81, 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.57: 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 SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 14 residues within 4Å: Chain A: I.64, G.65, A.67, R.70, P.83, M.84, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.65, A:G.65, A:A.67, A:M.84, A:R.85, A:S.86, A:D.89, A:D.138, A:D.138, A:Q.151, A:Q.151 Water bridges: A:R.41, A:R.85, A:R.85, A:R.85, A:R.85, A:Q.151 Salt bridges: A:R.41, A:R.70 SAH.8: 15 residues within 4Å: Chain B: I.64, G.65, A.67, R.70, P.83, M.84, R.85, D.89, R.92, T.137, D.138, Q.151, A.155, V.156 Ligands: MGP.9 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.65, B:G.65, B:M.84, B:R.85, B:S.86, B:D.89, B:D.138, B:D.138, B:Q.151, B:Q.151 Water bridges: B:R.41, B:A.67, B:R.85, B:R.85, B:R.85, B:R.85, B:Q.151 Salt bridges: B:R.41, B:R.70 SAH.13: 15 residues within 4Å: Chain C: I.64, G.65, A.67, R.70, P.83, M.84, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.14 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:G.65, C:G.65, C:A.67, C:M.84, C:R.85, C:S.86, C:D.89, C:D.138, C:D.138, C:Q.151, C:Q.151 Water bridges: C:R.41, C:R.85, C:R.85, C:R.85, C:R.85, C:Q.151 Salt bridges: C:R.41, C:R.70 SAH.18: 15 residues within 4Å: Chain D: I.64, G.65, A.67, R.70, P.83, M.84, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.19 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:G.65, D:G.65, D:A.67, D:M.84, D:R.85, D:S.86, D:D.89, D:D.138, D:D.138, D:Q.151, D:Q.151 Water bridges: D:R.41, D:R.85, D:R.85, D:R.85, D:R.85, D:Q.151 Salt bridges: D:R.41, D:R.70 SAH.23: 14 residues within 4Å: Chain E: I.64, G.65, A.67, R.70, P.83, M.84, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.24 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:G.65, E:G.65, E:A.67, E:M.84, E:R.85, E:R.85, E:S.86, E:D.89, E:D.138, E:D.138, E:Q.151, E:Q.151 Water bridges: E:R.41, E:R.71, E:T.137, E:Q.151 Salt bridges: E:R.41, E:R.70 SAH.28: 15 residues within 4Å: Chain F: G.65, A.67, R.70, P.83, M.84, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, A.155, V.156 Ligands: MGP.29 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:G.65, F:G.65, F:A.67, F:M.84, F:R.85, F:R.85, F:D.89, F:D.138, F:D.138, F:Q.151, F:Q.151 Water bridges: F:R.41, F:R.41, F:T.137, F:Q.151 Salt bridges: F:R.41, F:R.70 SAH.33: 16 residues within 4Å: Chain G: I.64, G.65, A.67, R.70, P.83, M.84, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: MGP.34 18 PLIP interactions: 18 interactions with chain G Hydrogen bonds: G:G.65, G:G.65, G:M.84, G:R.85, G:S.86, G:D.89, G:D.138, G:D.138, G:Q.151, G:Q.151 Water bridges: G:R.41, G:A.67, G:R.85, G:R.85, G:R.85, G:Q.151 Salt bridges: G:R.41, G:R.70 SAH.38: 14 residues within 4Å: Chain H: I.64, G.65, A.67, R.70, P.83, M.84, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.39 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:G.65, H:G.65, H:A.67, H:M.84, H:R.85, H:D.89, H:D.138, H:D.138, H:Q.151, H:Q.151 Water bridges: H:R.41, H:R.85, H:R.85, H:R.85, H:R.85, H:Q.151 Salt bridges: H:R.41, H:R.70 SAH.43: 16 residues within 4Å: Chain I: I.64, G.65, A.67, R.70, P.83, M.84, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: MGP.44 18 PLIP interactions: 18 interactions with chain I Hydrogen bonds: I:G.65, I:G.65, I:M.84, I:R.85, I:S.86, I:D.89, I:D.138, I:D.138, I:Q.151, I:Q.151 Water bridges: I:R.41, I:A.67, I:R.85, I:R.85, I:R.85, I:Q.151 Salt bridges: I:R.41, I:R.70 SAH.48: 15 residues within 4Å: Chain J: I.64, G.65, A.67, R.70, P.83, M.84, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.49 20 PLIP interactions: 20 interactions with chain J Hydrogen bonds: J:G.65, J:G.65, J:A.67, J:M.84, J:R.85, J:S.86, J:D.89, J:D.138, J:D.138, J:Q.151, J:Q.151 Water bridges: J:R.41, J:R.41, J:R.85, J:R.85, J:R.85, J:R.85, J:Q.151 Salt bridges: J:R.41, J:R.70 SAH.53: 15 residues within 4Å: Chain K: I.64, G.65, A.67, R.70, P.83, M.84, R.85, D.89, R.92, T.137, D.138, Q.151, A.155, V.156 Ligands: MGP.54 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:G.65, K:G.65, K:M.84, K:R.85, K:R.85, K:D.89, K:D.138, K:D.138, K:Q.151, K:Q.151 Water bridges: K:R.41, K:A.67, K:T.137, K:Q.151 Salt bridges: K:R.41, K:R.70 SAH.58: 14 residues within 4Å: Chain L: I.64, G.65, A.67, R.70, P.83, M.84, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.59 19 PLIP interactions: 19 interactions with chain L Hydrogen bonds: L:G.65, L:G.65, L:M.84, L:R.85, L:R.85, L:S.86, L:D.89, L:R.92, L:D.138, L:D.138, L:Q.151, L:Q.151 Water bridges: L:R.41, L:A.67, L:R.71, L:T.137, L:Q.151 Salt bridges: L:R.41, L:R.70

12 x MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

MGP.3: 16 residues within 4Å: Chain A: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain B: R.275 Ligands: SAH.2, MG.6 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.92, A:D.152, A:Y.285 Water bridges: A:N.35, A:R.41 Salt bridges: A:H.37, A:H.37, A:R.41, A:R.41, A:R.41, A:R.70, A:R.70, A:E.250, B:R.275, B:R.275 pi-Stacking: A:Y.248, A:Y.248 MGP.9: 17 residues within 4Å: Chain B: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.178, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain C: R.275 Ligands: SAH.8, MG.11 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.41, B:R.92, B:Y.285, B:Y.285 Water bridges: B:N.35, B:R.41 Salt bridges: B:H.37, B:H.37, B:R.41, B:R.41, B:R.41, B:R.70, B:R.70, B:E.250, C:R.275, C:R.275 pi-Stacking: B:Y.248 MGP.14: 17 residues within 4Å: Chain C: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.178, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain D: R.275 Ligands: SAH.13, MG.16 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.92, C:Y.285, C:Y.285 Water bridges: C:N.35, C:R.41 Salt bridges: C:H.37, C:H.37, C:R.41, C:R.41, C:R.41, C:R.70, C:R.70, C:E.250, D:R.275, D:R.275 pi-Stacking: C:Y.248, C:Y.248 MGP.19: 16 residues within 4Å: Chain D: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain E: R.275 Ligands: SAH.18, MG.21 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:R.92, D:Y.285, D:Y.285 Water bridges: D:N.35, D:R.41 Salt bridges: D:H.37, D:H.37, D:R.41, D:R.41, D:R.41, D:R.70, D:R.70, D:E.250, E:R.275, E:R.275 pi-Stacking: D:Y.248, D:Y.248 MGP.24: 17 residues within 4Å: Chain E: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.178, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain F: R.275 Ligands: SAH.23, MG.26 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:R.92, E:Y.285, E:Y.285 Water bridges: E:N.35, E:R.41 Salt bridges: E:H.37, E:H.37, E:R.41, E:R.41, E:R.41, E:R.70, E:R.70, E:E.250, F:R.275, F:R.275 pi-Stacking: E:Y.248 MGP.29: 16 residues within 4Å: Chain F: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain G: R.275 Ligands: SAH.28, MG.31 17 PLIP interactions: 15 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:R.92, F:Y.285, F:Y.285 Water bridges: F:N.35, F:R.41 Salt bridges: F:H.37, F:H.37, F:R.41, F:R.41, F:R.41, F:R.70, F:R.70, F:E.250, G:R.275, G:R.275 pi-Stacking: F:Y.248, F:Y.248 MGP.34: 16 residues within 4Å: Chain G: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain H: R.275 Ligands: SAH.33, MG.36 17 PLIP interactions: 15 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:R.92, G:Y.285, G:Y.285 Water bridges: G:N.35, G:R.41 Salt bridges: G:H.37, G:H.37, G:R.41, G:R.41, G:R.41, G:R.70, G:R.70, G:E.250, H:R.275, H:R.275 pi-Stacking: G:Y.248, G:Y.248 MGP.39: 16 residues within 4Å: Chain H: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain I: R.275 Ligands: SAH.38, MG.41 17 PLIP interactions: 15 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:R.92, H:D.152, H:Y.285 Water bridges: H:N.35, H:R.41, H:R.70 Salt bridges: H:H.37, H:H.37, H:R.41, H:R.41, H:R.41, H:R.70, H:R.70, H:E.250, I:R.275, I:R.275 pi-Stacking: H:Y.248 MGP.44: 17 residues within 4Å: Chain I: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.178, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain J: R.275 Ligands: SAH.43, MG.46 18 PLIP interactions: 16 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:R.41, I:R.92, I:D.152, I:Y.285 Water bridges: I:N.35, I:R.41 Salt bridges: I:H.37, I:H.37, I:R.41, I:R.41, I:R.41, I:R.70, I:R.70, I:E.250, J:R.275, J:R.275 pi-Stacking: I:Y.248, I:Y.248 MGP.49: 16 residues within 4Å: Chain J: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain K: R.275 Ligands: SAH.48, MG.51 17 PLIP interactions: 15 interactions with chain J, 2 interactions with chain K Hydrogen bonds: J:R.92, J:Y.285, J:Y.285 Water bridges: J:N.35, J:R.41 Salt bridges: J:H.37, J:H.37, J:R.41, J:R.41, J:R.41, J:R.70, J:R.70, J:E.250, K:R.275, K:R.275 pi-Stacking: J:Y.248, J:Y.248 MGP.54: 17 residues within 4Å: Chain K: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.178, F.241, V.243, T.246, Y.248, E.250, Y.285 Chain L: R.275 Ligands: SAH.53, MG.56 17 PLIP interactions: 15 interactions with chain K, 2 interactions with chain L Hydrogen bonds: K:R.92, K:Y.285, K:Y.285 Water bridges: K:N.35, K:R.41, K:R.70 Salt bridges: K:H.37, K:H.37, K:R.41, K:R.41, K:R.41, K:R.70, K:R.70, K:E.250, L:R.275, L:R.275 pi-Stacking: K:Y.248 MGP.59: 16 residues within 4Å: Chain A: R.275 Chain L: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, T.246, Y.248, E.250, Y.285 Ligands: MG.5, SAH.58 17 PLIP interactions: 15 interactions with chain L, 2 interactions with chain A Hydrogen bonds: L:N.35, L:R.92, L:Y.285, L:Y.285 Water bridges: L:R.41 Salt bridges: L:H.37, L:H.37, L:R.41, L:R.41, L:R.41, L:R.70, L:R.70, L:E.250, A:R.275, A:R.275 pi-Stacking: L:Y.248, L:Y.248

24 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.36, A:H.37 MG.5: 3 residues within 4Å: Chain A: D.277 Chain L: H.37 Ligands: MGP.59 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: H.37 Chain B: D.277 Ligands: MGP.3 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain B: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.36, B:H.37 MG.11: 3 residues within 4Å: Chain B: H.37 Chain C: D.277 Ligands: MGP.9 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain C: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.36, C:H.37 MG.16: 3 residues within 4Å: Chain C: H.37 Chain D: D.277 Ligands: MGP.14 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain D: D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.36, D:H.37 MG.21: 3 residues within 4Å: Chain D: H.37 Chain E: D.277 Ligands: MGP.19 No protein-ligand interaction detected (PLIP) MG.25: 6 residues within 4Å: Chain E: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.36, E:H.37 MG.26: 3 residues within 4Å: Chain E: H.37 Chain F: D.277 Ligands: MGP.24 No protein-ligand interaction detected (PLIP) MG.30: 6 residues within 4Å: Chain F: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.36, F:H.37 MG.31: 3 residues within 4Å: Chain F: H.37 Chain G: D.277 Ligands: MGP.29 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain G: D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.36, G:H.37 MG.36: 3 residues within 4Å: Chain G: H.37 Chain H: D.277 Ligands: MGP.34 No protein-ligand interaction detected (PLIP) MG.40: 6 residues within 4Å: Chain H: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.36, H:H.37 MG.41: 3 residues within 4Å: Chain H: H.37 Chain I: D.277 Ligands: MGP.39 No protein-ligand interaction detected (PLIP) MG.45: 6 residues within 4Å: Chain I: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.36, I:H.37 MG.46: 3 residues within 4Å: Chain I: H.37 Chain J: D.277 Ligands: MGP.44 No protein-ligand interaction detected (PLIP) MG.50: 6 residues within 4Å: Chain J: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.36, J:H.37 MG.51: 3 residues within 4Å: Chain J: H.37 Chain K: D.277 Ligands: MGP.49 No protein-ligand interaction detected (PLIP) MG.55: 6 residues within 4Å: Chain K: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.36, K:H.37 MG.56: 3 residues within 4Å: Chain K: H.37 Chain L: D.277 Ligands: MGP.54 No protein-ligand interaction detected (PLIP) MG.60: 6 residues within 4Å: Chain L: N.35, D.36, H.37, V.243, S.245, T.246 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.36, L:H.37

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: 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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