SMTL ID : 3jb7.1

In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 4.00 Å

Oligo State

hetero-1-1-2-mer

Ligands

1 x G- G- G- G- G- G: RNA (5'-R(P*GP*GP*GP*GP*GP*G)-3')(Non-covalent)

G-G-G-G-G-G.1: 29 residues within 4Å: Chain A: F.420, T.423, S.424, P.426, G.427, R.428, R.449, R.479, I.489, G.491, Q.519, K.521, Q.522, A.523, S.639, G.640, A.642, D.643, T.644, A.1077, S.1078, G.1081, P.1145 Ligands: C-C-C-C-C.2, C-C-C-C-C.2, C-C-C-C-C.2, C-C-C-C-C.2, C-C-C-C-C.2, CTP.4 Protein-ligand interaction information (PLIP) not available

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

C-C-C-C-C.2: 20 residues within 4Å: Chain A: R.141, L.678, G.679, D.680, L.723, Q.724, R.738, I.739, K.748, L.755, E.759, L.763, D.766, R.770 Ligands: G-G-G-G-G-G.1, G-G-G-G-G-G.1, G-G-G-G-G-G.1, G-G-G-G-G-G.1, G-G-G-G-G-G.1, CTP.4 Protein-ligand interaction information (PLIP) not available

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

GTP.3: 5 residues within 4Å: Chain A: R.37, R.147, Y.184, P.187, R.791 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.37, A:R.147 Salt bridges: A:R.37 pi-Stacking: A:Y.184 pi-Cation interactions: A:Y.184 GTP.5: 9 residues within 4Å: Chain B: K.355, G.356, G.358, K.359, T.360, S.361, R.520, Q.521, R.522 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.356, B:G.358, B:K.359, B:T.360, B:S.361, B:R.520, B:R.520, B:Q.521, B:R.522 Salt bridges: B:K.355, B:K.359

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.4: 15 residues within 4Å: Chain A: R.479, R.487, I.489, V.548, A.549, G.550, M.551, D.552, S.639, T.644, H.648, D.680 Ligands: G-G-G-G-G-G.1, G-G-G-G-G-G.1, C-C-C-C-C.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.489 Hydrogen bonds: A:R.479, A:R.487, A:V.548, A:G.550, A:H.648, A:D.680 Salt bridges: A:R.487

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus. Nature (2015)

Release Date

2015-10-28

Peptides

CPV RNA-dependent RNA polymerase: A
Viral structural protein 4: B
VP1 CSP: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CPV RNA-dependent RNA polymerase

Viral structural protein 4

VP1 CSP

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