› 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
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
Molecule details ›
Chains: D, N
Length: 1524 amino acids
Theoretical weight: 171 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8RQE8 (Residues: 1-1524; Coverage: 100%)
Gene names: TTHA1812, rpoC
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit omega Chains: E, O
Molecule details ›
Chains: E, O
Length: 99 amino acids
Theoretical weight: 11.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8RQE7 (Residues: 1-99; Coverage: 100%)
Gene names: TTHA1561, rpoZ
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
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
Molecule details ›
Chains: G, X
Length: 23 nucleotides
Theoretical weight: 7 KDa
DNA (5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3') Chains: I, Z
Molecule details ›
Chains: I, Z
Length: 14 nucleotides
Theoretical weight: 4.32 KDa
RNA (5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3') Chains: H, Y
Molecule details ›
Chains: H, Y
Length: 16 nucleotides
Theoretical weight: 5.18 KDa

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

Entry percentile scores
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

Quick links

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