› 3vwb

X-ray diffraction
2.42Å resolution

Crystal structure of VirB core domain (Se-Met derivative) complexed with the cis-acting site (5-BRU modifications) upstream icsb promoter

Released:
DOI: 10.2210/pdb3vwb/pdb
PDB entry 3vwb coloured by chain, front view.
PDB entry 3vwb coloured by chain, side view.
PDB entry 3vwb coloured by chain, top view.
Source organism: Shigella flexneri 2a
Primary publication:
Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes.
Gao X, Zou T, Mu Z, Qin B, Yang J, Waltersperger S, Wang M, Cui S, Jin Q
Nucleic Acids Res 41 10529-41 (2013)
PMID: 23985969

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117063 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Virulence regulon transcriptional activator VirB Chain: A
Molecule details ›
Chain: A
Length: 143 amino acids
Theoretical weight: 16.25 KDa
Source organism: Shigella flexneri 2a
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A247 (Residues: 129-250; Coverage: 40%)
Gene names: CP0123, invE, virB
Sequence domains: ParB family
Structure domains: Arc Repressor Mutant, subunit A
DNA (26-MER) Chain: C
Molecule details ›
Chain: C
Length: 26 nucleotides
Theoretical weight: 8 KDa
Source organism: Shigella flexneri 2a
Expression system: Not provided
DNA (26-MER) Chain: B
Molecule details ›
Chain: B
Length: 26 nucleotides
Theoretical weight: 8.1 KDa
Source organism: Shigella flexneri 2a
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand BRU 2 x BRU

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21212
Unit cell:
a: 57.321Å b: 163.051Å c: 39.569Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.235 0.271
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Integrated circuits: how transcriptional silencing and counter-silencing facilitate bacterial evolution.
Will et al. (2015)
2 more

3 mentions without citation

Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly.
Braun et al. (2017)
2 more