SMTL ID : 9gju.1

Structure of replicating Nipah Virus RNA Polymerase Complex - RNA-bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-mer

Ligands

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

A-C-C-A-A-A-C-A-A.1: 29 residues within 4Å: Chain D: U.4, U.5, G.6, U.7, U.8, U.9, G.10, G.11, U.12 Chain E: D.20, R.363, D.468, S.470, K.474, K.546, Q.805, Q.832, G.833, D.834, N.835, S.894, K.895, K.909, R.913, E.919, N.931, E.1135, G.1138 Ligands: GNP.2 25 PLIP interactions: 25 interactions with chain E Hydrogen bonds: E:A.477, E:R.505, E:R.506, E:K.544, E:K.544, E:Q.566, E:E.590, E:Y.803, E:K.806, E:S.930, E:K.938, E:R.1008, E:R.1012, E:N.1013, E:Q.1068, E:S.1069, E:S.1069 Salt bridges: E:K.476, E:K.476, E:R.505, E:R.563, E:K.806, E:R.1008, E:R.1012 pi-Stacking: E:F.555

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 18 residues within 4Å: Chain D: C.3 Chain E: K.544, R.553, D.724, L.725, K.726, K.727, F.728, C.729, E.801, G.802, Q.805, W.808, D.834, K.880, E.883 Ligands: A-C-C-A-A-A-C-A-A.1, MG.5 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:K.544, E:R.553, E:R.553, E:L.725, E:K.727, E:K.727, E:F.728, E:E.801, E:G.802, E:Q.805, E:K.880, E:K.880 Salt bridges: E:R.553, E:E.801

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain E: C.1238, C.1241, H.1423, H.1425 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.1238, E:C.1241, E:H.1423, E:H.1425 ZN.4: 4 residues within 4Å: Chain E: C.1193, E.1225, C.1430, C.1431 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.1193, E:E.1225, E:C.1430, E:C.1431

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain E: D.724, L.725, D.834 Ligands: GNP.2 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.724, E:L.725, E:D.834

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sala, F.A. et al., Structural basis of Nipah virus RNA synthesis. Nat Commun (2025)

Release Date

2025-03-05

Peptides

Phosphoprotein: ABCF
RNA-directed RNA polymerase L: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

F
B

E
A

Phosphoprotein

RNA-directed RNA polymerase L

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