› 4jk2

X-ray diffraction
4.2Å resolution

X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with guanosine pentaphosphate (pppGpp)

Released:
DOI: 10.2210/pdb4jk2/pdb
Model geometry
Fit model/data
PDB entry 4jk2 coloured by chain, front view.
PDB entry 4jk2 coloured by chain, side view.
PDB entry 4jk2 coloured by chain, top view.
Source organisms:
Primary publication:
Differential regulation by ppGpp versus pppGpp in Escherichia coli.
Mechold U, Potrykus K, Murphy H, Murakami KS, Cashel M
OpenAccess logo Nucleic Acids Res 41 6175-89 (2013)
PMID: 23620295

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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132730 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, F, G
Molecule details ›
Chains: A, B, F, G
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
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, H
Molecule details ›
Chains: C, H
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
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, I
DNA-directed RNA polymerase subunit omega Chains: E, J
RNA polymerase sigma factor RpoD Chains: X, Y

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand 0O2 1 x 0O2
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: CHESS BEAMLINE A1
Spacegroup: P212121
Unit cell:
a: 185.323Å b: 205.411Å c: 309.581Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.244 0.322
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

30 review citations

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

4 mentions without citation

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