› 7zla

Electron Microscopy
3.99Å resolution

Cryo-EM structure of holo-PdxR from Bacillus clausii bound to its target DNA in the half-closed conformation

Released:
DOI: 10.2210/pdb7zla/pdb
PDB entry 7zla coloured by chain, front view.
PDB entry 7zla coloured by chain, side view.
PDB entry 7zla coloured by chain, top view.
Source organism: Alkalihalobacillus clausii
Primary publication:
Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR.
Freda I, Exertier C, Barile A, Chaves-Sanjuan A, Vega MV, Isupov MN, Harmer NJ, Gugole E, Swuec P, Bolognesi M, Scipioni A, Savino C, Di Salvo ML, Contestabile R, Vallone B, Tramonti A, Montemiglio LC
OpenAccess logo Nucleic Acids Res 51 8237-8254 (2023)
PMID: 37378428
Related structures: EMD-14778

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-235628 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
HTH gntR-type domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 478 amino acids
Theoretical weight: 55.5 KDa
Source organism: Alkalihalobacillus clausii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5WKW3 (Residues: 1-464; Coverage: 100%)
Gene name: ABC0450
Sequence domains:
DNA (48-MER) Chain: C
Molecule details ›
Chain: C
Length: 48 nucleotides
Theoretical weight: 14.67 KDa
Source organism: Alkalihalobacillus clausii
Expression system: Not provided
DNA (48-MER) Chain: D
Molecule details ›
Chain: D
Length: 48 nucleotides
Theoretical weight: 14.89 KDa
Source organism: Alkalihalobacillus clausii
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.99Å
Relevant EMDB volumes: EMD-14778
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 citations in other articles

Promoter DNA recognition by the Enterococcus faecalis global regulator MafR.
Moreno-Blanco et al. (2023)