› 5w1t

X-ray diffraction
4.5Å resolution

X-ray crystal structure of Escherichia coli RNA polymerase and DksA complex

Released:
DOI: 10.2210/pdb5w1t/pdb
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PDB entry 5w1t coloured by chain, front view.
PDB entry 5w1t coloured by chain, side view.
PDB entry 5w1t coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.
Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS
Mol Cell 69 828-839.e5 (2018)
PMID: 29478808

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 heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132731 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, G, H
Molecule details ›
Chains: A, B, G, H
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chains: C, I
Molecule details ›
Chains: C, I
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8V2 (Residues: 1-1342; Coverage: 100%)
Gene names: JW3950, b3987, groN, nitB, rif, ron, rpoB, stl, stv, tabD
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chains: D, J
DNA-directed RNA polymerase subunit omega Chains: E, K
RNA polymerase sigma factor RpoD Chains: F, L
RNA polymerase-binding transcription factor DksA Chains: M, N

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 184Å b: 204.894Å c: 314.312Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.22 0.276
Expression system: Escherichia coli

Quick links

Citations

15 review citations

The stringent response and physiological roles of (pp)pGpp in bacteria.
Irving et al. (2021)
14 more

3 mentions without citation

Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.
Molodtsov et al. (2018)
2 more

PDB-REDO

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