› 5zjq

X-ray diffraction
2.44Å resolution

Structure of AbdB/Exd complex bound to a 'Red14' DNA sequence

Released:
DOI: 10.2210/pdb5zjq/pdb
PDB entry 5zjq coloured by chain, front view.
PDB entry 5zjq coloured by chain, side view.
PDB entry 5zjq coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.
Zeiske T, Baburajendran N, Kaczynska A, Brasch J, Palmer AG, Shapiro L, Honig B, Mann RS
Cell Rep 24 2221-2230 (2018)
PMID: 30157419

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119508 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Homeobox protein abdominal-B Chain: A
Molecule details ›
Chain: A
Length: 84 amino acids
Theoretical weight: 10.2 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P09087 (Residues: 369-452; Coverage: 17%)
Gene names: Abd-B, CG10291
Sequence domains: Homeodomain
Structure domains: Homeodomain-like
Homeobox protein extradenticle Chain: B
Molecule details ›
Chain: B
Length: 74 amino acids
Theoretical weight: 8.77 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P40427 (Residues: 237-310; Coverage: 20%)
Gene names: CG8933, exd
Sequence domains: Homeobox KN domain
Structure domains: Homeodomain-like
DNA (5'-D(*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*AP*TP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*TP*TP*AP*TP*GP*AP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 14 nucleotides
Theoretical weight: 4.29 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: C2
Unit cell:
a: 77.056Å b: 49.44Å c: 95.194Å
α: 90° β: 109.33° γ: 90°
R-values:
R R work R free
0.226 0.223 0.252
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.
Kribelbauer et al. (2019)
3 more

2 mentions without citation

Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.
Zeiske et al. (2018)
1 more