› 3aoi

X-ray diffraction
4.3Å resolution

RNA polymerase-Gfh1 complex (Crystal type 2)

Released:
DOI: 10.2210/pdb3aoi/pdb
PDB entry 3aoi coloured by chain, front view.
PDB entry 3aoi coloured by chain, side view.
PDB entry 3aoi coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
Tagami S, Sekine S, Kumarevel T, Hino N, Murayama Y, Kamegamori S, Yamamoto M, Sakamoto K, Yokoyama S
Nature 468 978-82 (2010)
PMID: 21124318

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 octamer (preferred)
PDBe Complex ID:
PDB-CPX-116069 (preferred)
Entry contents:
5 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (7 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, F, G, K, L
Molecule details ›
Chains: A, B, F, G, 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:
DNA-directed RNA polymerase subunit beta Chains: C, H, M
Molecule details ›
Chains: C, H, 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:
DNA-directed RNA polymerase subunit beta' Chains: D, I, N
Molecule details ›
Chains: D, I, 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:
DNA-directed RNA polymerase subunit omega Chains: E, J, O
Molecule details ›
Chains: E, J, 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
Transcription inhibitor protein Gfh1 Chains: X, Y, Z
Molecule details ›
Chains: X, Y, Z
Length: 156 amino acids
Theoretical weight: 17.21 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SJG6 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1042, gfh1
Sequence domains:
DNA (5'-D(*GP*GP*TP*CP*TP*GP*TP*AP*TP*CP*AP*CP*GP*AP*GP*CP*CP*A*CP*CP*GP*CP*CP*GP*CP*AP*T)-3') Chains: P, R, T
Molecule details ›
Chains: P, R, T
Length: 27 nucleotides
Theoretical weight: 8.24 KDa
RNA (5'-R(*CP*CP*CP*GP*GP*AP*AP*GP*AP*UP*CP*AP*UP*CP*UP*UP*CP*CP*GP*GP*GP*GP*GP*AP*U*GP*CP*GP*GP*CP*GP*G)-3') Chains: Q, S, U
Molecule details ›
Chains: Q, S, U
Length: 32 nucleotides
Theoretical weight: 10.37 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 189.23Å b: 264.51Å c: 193.93Å
α: 90° β: 116.68° γ: 90°
R-values:
R R work R free
0.317 0.317 0.338
Expression system: Escherichia coli

Quick links

Citations

28 review citations

Recent functional insights into the role of (p)ppGpp in bacterial physiology.
Hauryliuk et al. (2015)
27 more

5 mentions without citation

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