› 4xln

X-ray diffraction
4Å resolution

Crystal structure of T. aquaticus transcription initiation complex containing bubble promoter and RNA

Released:
DOI: 10.2210/pdb4xln/pdb
PDB entry 4xln coloured by chain, front view.
PDB entry 4xln coloured by chain, side view.
PDB entry 4xln coloured by chain, top view.
Source organism: Thermus aquaticus
Primary publication:
Structure of a bacterial RNA polymerase holoenzyme open promoter complex.
Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA
Elife 4 (2015)
PMID: 26349032

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 nonamer (preferred)
PDBe Complex ID:
PDB-CPX-118265 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (8 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, G, H
Molecule details ›
Chains: A, B, G, H
Length: 314 amino acids
Theoretical weight: 34.83 KDa
Source organism: Thermus aquaticus
UniProt:
  • Canonical: Q9KWU8 (Residues: 1-314; Coverage: 100%)
Gene name: rpoA
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit beta Chains: C, I
Molecule details ›
Chains: C, I
Length: 1119 amino acids
Theoretical weight: 124.93 KDa
Source organism: Thermus aquaticus
UniProt:
  • Canonical: Q9KWU7 (Residues: 1-1119; Coverage: 100%)
Gene name: rpoB
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chains: D, J
Molecule details ›
Chains: D, J
Length: 1524 amino acids
Theoretical weight: 171.19 KDa
Source organism: Thermus aquaticus
UniProt:
  • Canonical: Q9KWU6 (Residues: 1-1524; Coverage: 100%)
Gene name: rpoC
Sequence domains:
DNA-directed RNA polymerase subunit omega Chains: E, K
Molecule details ›
Chains: E, K
Length: 99 amino acids
Theoretical weight: 11.64 KDa
Source organism: Thermus aquaticus
UniProt:
  • Canonical: Q9EVV4 (Residues: 1-99; Coverage: 100%)
Gene name: rpoZ
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
RNA polymerase sigma factor SigA Chains: F, L
Molecule details ›
Chains: F, L
Length: 347 amino acids
Theoretical weight: 39.86 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9EZJ8 (Residues: 92-438; Coverage: 79%)
Gene name: sigA
Sequence domains:
Structure domains:
DNA (48-MER) Chains: O, R
Molecule details ›
Chains: O, R
Length: 48 nucleotides
Theoretical weight: 14.88 KDa
DNA (48-MER) Chains: P, S
Molecule details ›
Chains: P, S
Length: 48 nucleotides
Theoretical weight: 14.83 KDa
RNA (5'-D(P*UP*CP*GP*A)-3') Chains: Q, T
Molecule details ›
Chains: Q, T
Length: 4 nucleotides
Theoretical weight: 1.24 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P43212
Unit cell:
a: 289.259Å b: 289.259Å c: 536.601Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.282 0.28 0.315
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

18 review citations

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer.
Lerner et al. (2018)
17 more

18 mentions without citation

Bacterial RNA Polymerase-DNA Interaction-The Driving Force of Gene Expression and the Target for Drug Action.
Lee et al. (2016)
17 more