› 4s20

X-ray diffraction
4.7Å resolution

Structural basis for transcription reactivation by RapA

Released:
DOI: 10.2210/pdb4s20/pdb
PDB entry 4s20 coloured by chain, front view.
PDB entry 4s20 coloured by chain, side view.
PDB entry 4s20 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural basis for transcription reactivation by RapA.
Liu B, Zuo Y, Steitz TA
Proc Natl Acad Sci U S A 112 2006-10 (2015)
PMID: 25646438

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-118158 (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
Molecule details ›
Chains: A, B, F, G
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli
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, H
Molecule details ›
Chains: C, H
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli
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, I
Molecule details ›
Chains: D, I
Length: 1416 amino acids
Theoretical weight: 156.54 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
DNA-directed RNA polymerase subunit omega Chains: E, J
Molecule details ›
Chains: E, J
Length: 90 amino acids
Theoretical weight: 10.12 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
RNA polymerase-associated protein RapA Chains: K, L
Molecule details ›
Chains: K, L
Length: 974 amino acids
Theoretical weight: 110.67 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P60240 (Residues: 1-968; Coverage: 100%)
Gene names: JW0058, b0059, hepA, rapA, yabA
Sequence domains:
5'-D(P*AP*CP*GP*AP*CP*TP*GP*AP*GP*CP*CP*GP*AP*TP*G)-3' Chains: M, O
Molecule details ›
Chains: M, O
Length: 15 nucleotides
Theoretical weight: 4.62 KDa
5'-R(P*AP*UP*CP*GP*GP*CP*UP*CP*A)-3' Chains: N, P
Molecule details ›
Chains: N, P
Length: 9 nucleotides
Theoretical weight: 2.83 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 X25
Spacegroup: C2
Unit cell:
a: 336.09Å b: 158.93Å c: 255.01Å
α: 90° β: 101.28° γ: 90°
R-values:
R R work R free
0.278 0.273 0.369
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Bacterial Transcription as a Target for Antibacterial Drug Development.
Ma et al. (2016)
3 more

7 mentions without citation

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