› 4mex

X-ray diffraction
3.9Å resolution

Crystal structure of Escherichia coli RNA polymerase in complex with salinamide A

Released:
DOI: 10.2210/pdb4mex/pdb
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PDB entry 4mex coloured by chain, front view.
PDB entry 4mex coloured by chain, side view.
PDB entry 4mex coloured by chain, top view.
Source organisms:
Primary publication:
Transcription inhibition by the depsipeptide antibiotic salinamide A.
Degen D, Feng Y, Zhang Y, Ebright KY, Ebright YW, Gigliotti M, Vahedian-Movahed H, Mandal S, Talaue M, Connell N, Arnold E, Fenical W, Ebright RH
OpenAccess logo Elife 3 e02451 (2014)
PMID: 24843001

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-132733 (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: 335 amino acids
Theoretical weight: 37.39 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7Z4 (Residues: 2-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
Structure 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:
Structure 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
Salinamide A Chains: M, N

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ZN 4 x ZN
3 modified residues:
Ligand D4P 2 x D4P
Ligand MEA 2 x MEA
Ligand 2TL 2 x 2TL

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 185.8Å b: 208.188Å c: 308.179Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.287 0.286 0.325
Expression systems:
  • Escherichia coli
  • Not provided

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Citations

15 review citations

Actinomycetes: still a source of novel antibiotics.
Genilloud O. (2017)
14 more

8 mentions without citation

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

PDB-REDO

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