SMTL ID : 6rie.1

Structure of Vaccinia Virus DNA-dependent RNA polymerase co-transcriptional capping complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.415, D.417, D.419 Chain K: G.30 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.417, A:D.419, A:D.419 MG.7: 5 residues within 4Å: Chain J: E.37, E.39, E.192, E.194 Chain K: G.1 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:E.39, J:E.192, J:E.194

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.49, C.52, C.59, H.62 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.49, A:C.52, A:C.59, A:H.62 ZN.3: 5 residues within 4Å: Chain A: C.90, C.93, C.130, N.132, C.135 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.90, A:C.93, A:C.130, A:C.135 ZN.4: 5 residues within 4Å: Chain B: C.1087, C.1090, D.1092, C.1103, C.1106 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1087, B:C.1090, B:C.1103, B:C.1106 ZN.5: 4 residues within 4Å: Chain G: C.7, C.10, C.39, C.40 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.39, G:C.40

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.6: 17 residues within 4Å: Chain J: R.548, L.549, Y.555, F.556, K.573, D.598, F.599, G.600, D.604, D.620, P.621, D.622, R.655, Q.678, F.679, A.680, Y.683 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:R.548, J:L.549, J:L.549, J:D.598, J:D.622, J:D.622, J:R.655, J:Q.678 Salt bridges: J:K.573 pi-Stacking: J:Y.683 pi-Cation interactions: J:R.548

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hillen, H.S. et al., Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes. Cell (2019)

Release Date

2019-12-18

Peptides

DNA-dependent RNA polymerase subunit rpo147: A
DNA-dependent RNA polymerase subunit rpo132: B
DNA-directed RNA polymerase 35 kDa subunit: C
DNA-directed RNA polymerase subunit: D
DNA-directed RNA polymerase 19 kDa subunit: E
DNA-dependent RNA polymerase subunit rpo18: F
DNA-dependent RNA polymerase subunit rpo7: G
Small subunit of mRNA capping enzyme: H
Large subunit of mRNA capping enzyme: J
DNA-directed RNA polymerase 30 kDa polypeptide: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
G

G
J

H
L

J
O

L
S

DNA-dependent RNA polymerase subunit rpo147

DNA-dependent RNA polymerase subunit rpo132

DNA-directed RNA polymerase 35 kDa subunit

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase 19 kDa subunit

DNA-dependent RNA polymerase subunit rpo18

DNA-dependent RNA polymerase subunit rpo7

Small subunit of mRNA capping enzyme

Large subunit of mRNA capping enzyme

DNA-directed RNA polymerase 30 kDa polypeptide

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