› 2ppb

X-ray diffraction
3Å resolution

Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin

Released:
DOI: 10.2210/pdb2ppb/pdb
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PDB entry 2ppb coloured by chain, front view.
PDB entry 2ppb coloured by chain, side view.
PDB entry 2ppb coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Structural basis for substrate loading in bacterial RNA polymerase.
Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R
Nature 448 163-8 (2007)
PMID: 17581591

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115775 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (7 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, K, L
Molecule details ›
Chains: A, B, K, L
Length: 315 amino acids
Theoretical weight: 35.06 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR6 (Residues: 1-315; Coverage: 100%)
Gene names: TTHA1664, rpoA
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit beta Chains: C, M
Molecule details ›
Chains: C, M
Length: 1119 amino acids
Theoretical weight: 125.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8RQE9 (Residues: 1-1119; Coverage: 100%)
Gene names: TTHA1813, rpoB
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit beta' Chains: D, N
DNA-directed RNA polymerase subunit omega Chains: E, O
DNA (5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3') Chains: G, X
DNA (5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3') Chains: I, Z
RNA (5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3') Chains: H, Y

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P41
Unit cell:
a: 155.379Å b: 155.379Å c: 496.992Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.234 0.266

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Citations

39 review citations

Structure of eukaryotic RNA polymerases.
Cramer et al. (2008)
38 more

21 mentions without citation

Structural biology of bacterial RNA polymerase.
Murakami KS. (2015)
20 more

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