SMTL ID : 9fpy.1

Structure of the complete Vaccinia DNA-dependent RNA polymerase complex assembly intermediate 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-2-1-1-1-1-1-1-mer

Ligands

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 2 residues within 4Å: Chain G: U.8, G.9 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain G: U.47, A.58 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain H: D.415, D.417, D.419 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.415, H:D.417, H:D.417, H:D.419 MG.8: 2 residues within 4Å: Chain G: U.35 Chain M: R.120 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 7 residues within 4Å: Chain H: G.42, C.49, T.51, C.52, C.59, G.61, H.62 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.49, H:C.52, H:C.59, H:H.62 ZN.5: 6 residues within 4Å: Chain H: C.90, H.92, C.93, C.130, N.132, C.135 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.90, H:C.93, H:C.130, H:C.135 ZN.6: 6 residues within 4Å: Chain I: C.1087, N.1089, C.1090, C.1103, C.1106, P.1113 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.1087, I:C.1090, I:C.1103, I:C.1106 ZN.7: 5 residues within 4Å: Chain K: C.326, H.328, C.363, V.365, C.366 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.326, K:H.328, K:C.363, K:C.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grimm, C. et al., Structure of the complete Vaccinia DNA-dependent RNA polymerase complex at 2.65A resolution. To Be Published

Release Date

2025-06-25

Peptides

DNA-directed RNA polymerase 35 kDa subunit: A
DNA-directed RNA polymerase 22 kDa subunit: B
DNA-directed RNA polymerase 18 kDa subunit: C
DNA-directed RNA polymerase 7 kDa subunit: D
Core protein OPG073: EF
DNA-directed RNA polymerase 147 kDa polypeptide: H
DNA-directed RNA polymerase 133 kDa polypeptide: I
DNA-directed RNA polymerase 19 kDa subunit: J
RNA polymerase-associated transcription-specificity factor RAP94: K
DNA-directed RNA polymerase 30 kDa polypeptide: L
Nucleoside triphosphatase I: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
G

D
J

E
Q

F
R

H
A

I
B

J
F

K
I

L
S

M
Y

DNA-directed RNA polymerase 35 kDa subunit

DNA-directed RNA polymerase 22 kDa subunit

DNA-directed RNA polymerase 18 kDa subunit

DNA-directed RNA polymerase 7 kDa subunit

Core protein OPG073

DNA-directed RNA polymerase 147 kDa polypeptide

DNA-directed RNA polymerase 133 kDa polypeptide

DNA-directed RNA polymerase 19 kDa subunit

RNA polymerase-associated transcription-specificity factor RAP94

DNA-directed RNA polymerase 30 kDa polypeptide

Nucleoside triphosphatase I

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