SMTL ID : 3l25.1

Crystal structure of Zaire Ebola VP35 interferon inhibitory domain bound to 8 bp dsRNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

2 x C- G- C- A- U- G- C- G: RNA (5'-R(*CP*GP*CP*AP*UP*GP*CP*G)-3')(Non-covalent)

C-G-C-A-U-G-C-G.1: 40 residues within 4Å: Chain A: F.28, S.61, Q.63, C.64, I.67, I.129 Chain B: I.67, Q.68, K.71, R.101, R.111, I.129 Chain C: P.22, G.23, T.26, A.95, K.98, S.99 Chain D: F.28, Q.63, I.67, I.129 Ligands: C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2, FMT.11, FMT.20, NA.22, NA.23, NA.24, FMT.25, FMT.26, FMT.30, NA.39, FMT.40 Protein-ligand interaction information (PLIP) not available C-G-C-A-U-G-C-G.2: 38 residues within 4Å: Chain A: P.22, G.23, T.26, A.95, K.98, S.99 Chain B: F.28, Q.63, I.67, I.129 Chain C: F.28, S.61, Q.63, C.64, I.67, I.129 Chain D: C.64, I.67, Q.68, K.71, R.101, R.111 Ligands: C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.1, GOL.6, NA.22, NA.23, FMT.25, FMT.26, FMT.32, NA.39, FMT.40 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: G.25, H.29, P.93 Ligands: FMT.8, FMT.9 No protein-ligand interaction detected (PLIP)

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.89, L.119 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: Q.53 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain C: D.19, H.20 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain D: S.88, R.89 Ligand excluded by PLIP

8 x NA: SODIUM ION(Non-functional Binders)

NA.5: 4 residues within 4Å: Chain A: L.21, P.22, G.23, F.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.29 NA.13: 4 residues within 4Å: Chain B: L.21, P.22, G.23, F.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.18 NA.14: 3 residues within 4Å: Chain B: P.104, P.105, P.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.105 NA.22: 4 residues within 4Å: Ligands: C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.2, FMT.11, FMT.32 No protein-ligand interaction detected (PLIP) NA.23: 3 residues within 4Å: Ligands: C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.2 No protein-ligand interaction detected (PLIP) NA.24: 2 residues within 4Å: Chain C: S.99 Ligands: C-G-C-A-U-G-C-G.1 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.99 NA.28: 4 residues within 4Å: Chain C: L.21, P.22, G.23, F.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.18 NA.39: 3 residues within 4Å: Ligands: C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: R.94 Chain D: R.101, W.113, K.128 Ligands: C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.94, A:R.94 Water bridges: A:F.24

24 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 3 residues within 4Å: Chain A: F.24, R.94 Chain D: P.105 Ligand excluded by PLIP FMT.8: 6 residues within 4Å: Chain A: Y.18, H.29, Q.30, Q.33 Ligands: MG.3, FMT.9 Ligand excluded by PLIP FMT.9: 5 residues within 4Å: Chain A: F.24, G.25, H.29 Ligands: MG.3, FMT.8 Ligand excluded by PLIP FMT.10: 2 residues within 4Å: Chain A: P.82, V.83 Ligand excluded by PLIP FMT.11: 4 residues within 4Å: Chain A: P.22, Q.63 Ligands: C-G-C-A-U-G-C-G.1, NA.22 Ligand excluded by PLIP FMT.15: 4 residues within 4Å: Chain B: G.90, D.91, I.92, P.93 Ligand excluded by PLIP FMT.16: 5 residues within 4Å: Chain B: S.106, P.107, K.108, R.111, W.113 Ligand excluded by PLIP FMT.17: 3 residues within 4Å: Chain A: S.106 Chain B: A.54, E.58 Ligand excluded by PLIP FMT.18: 8 residues within 4Å: Chain B: G.25, T.26, H.29, Q.30, Q.33, P.93, C.96 Ligands: FMT.19 Ligand excluded by PLIP FMT.19: 5 residues within 4Å: Chain B: Y.18, F.24, G.25, H.29 Ligands: FMT.18 Ligand excluded by PLIP FMT.20: 3 residues within 4Å: Chain B: K.71, D.110 Ligands: C-G-C-A-U-G-C-G.1 Ligand excluded by PLIP FMT.21: 5 residues within 4Å: Chain B: T.70, K.71, R.72, V.73, Q.77 Ligand excluded by PLIP FMT.25: 4 residues within 4Å: Chain C: F.28 Ligands: C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.2 Ligand excluded by PLIP FMT.26: 4 residues within 4Å: Chain A: F.28 Ligands: C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2 Ligand excluded by PLIP FMT.29: 5 residues within 4Å: Chain C: N.43, S.44, L.45, D.46, I.47 Ligand excluded by PLIP FMT.30: 3 residues within 4Å: Chain B: W.113 Chain C: R.94 Ligands: C-G-C-A-U-G-C-G.1 Ligand excluded by PLIP FMT.31: 3 residues within 4Å: Chain B: P.105 Chain C: F.24, R.94 Ligand excluded by PLIP FMT.32: 5 residues within 4Å: Chain C: P.22, P.62, Q.63 Ligands: C-G-C-A-U-G-C-G.2, NA.22 Ligand excluded by PLIP FMT.33: 2 residues within 4Å: Chain C: L.38, P.82 Ligand excluded by PLIP FMT.35: 3 residues within 4Å: Chain D: Q.30, K.37, P.82 Ligand excluded by PLIP FMT.36: 3 residues within 4Å: Chain D: F.24, R.94, A.95 Ligand excluded by PLIP FMT.37: 2 residues within 4Å: Chain D: D.121, G.122 Ligand excluded by PLIP FMT.38: 1 residues within 4Å: Chain D: P.22 Ligand excluded by PLIP FMT.40: 3 residues within 4Å: Ligands: C-G-C-A-U-G-C-G.1, C-G-C-A-U-G-C-G.2, C-G-C-A-U-G-C-G.2 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leung, D.W. et al., Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-01-26

Peptides

Polymerase cofactor VP35: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

Polymerase cofactor VP35

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