› 4qiw

X-ray diffraction
3.5Å resolution

Crystal structure of euryarchaeal RNA polymerase from Thermococcus kodakarensis

Released:
DOI: 10.2210/pdb4qiw/pdb
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Source organism: Thermococcus kodakarensis KOD1
Primary publication:
The X-ray crystal structure of the euryarchaeal RNA polymerase in an open-clamp configuration.
Jun SH, Hirata A, Kanai T, Santangelo TJ, Imanaka T, Murakami KS
OpenAccess logo Nat Commun 5 5132 (2014)
PMID: 25311937

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177271 (preferred)
Entry contents:
11 distinct polypeptide molecules
Macromolecules (11 distinct):
DNA-directed RNA polymerase subunit Rpo1N Chains: A, I
Molecule details ›
Chains: A, I
Length: 906 amino acids
Theoretical weight: 103.04 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JE33 (Residues: 1-906; Coverage: 100%)
Gene names: TK1082, rpo1N, rpoA1
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit beta Chains: B, J
Molecule details ›
Chains: B, J
Length: 1123 amino acids
Theoretical weight: 127.47 KDa
Source organism: Thermococcus kodakarensis KOD1
UniProt:
  • Canonical: Q5JE32 (Residues: 1-1123; Coverage: 100%)
Gene name: TK1083
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit Rpo1C Chains: C, M
DNA-directed RNA polymerase subunit Rpo3 Chains: D, O
DNA-directed RNA polymerase subunit Rpo7 Chains: E, Q
DNA-directed RNA polymerase subunit Rpo4 Chains: F, R
DNA-directed RNA polymerase subunit Rpo5 Chains: H, S
DNA-directed RNA polymerase subunit Rpo6 Chains: K, T
DNA-directed RNA polymerase subunit Rpo11 Chains: L, U
DNA-directed RNA polymerase subunit Rpo10 Chains: N, V
DNA-directed RNA polymerase subunit Rpo12 Chains: P, W

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand ZN 10 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 112.975Å b: 206.606Å c: 365.157Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.279 0.277 0.316

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Citations

6 review citations

Molecular Mechanisms of Transcription Initiation-Structure, Function, and Evolution of TFE/TFIIE-Like Factors and Open Complex Formation.
Blombach et al. (2016)
5 more

10 mentions without citation

Transcription Regulation in Archaea.
Gehring et al. (2016)
9 more

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