› 2d5v

X-ray diffraction
2Å resolution

Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter

Released:
DOI: 10.2210/pdb2d5v/pdb
PDB entry 2d5v coloured by chain, front view.
PDB entry 2d5v coloured by chain, side view.
PDB entry 2d5v coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
DNA recognition mechanism of the ONECUT homeodomain of transcription factor HNF-6.
Iyaguchi D, Yao M, Watanabe N, Nishihira J, Tanaka I
Structure 15 75-83 (2007)
PMID: 17223534

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-115158 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Hepatocyte nuclear factor 6 Chains: A, B
Molecule details ›
Chains: A, B
Length: 164 amino acids
Theoretical weight: 19.66 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P70512 (Residues: 289-444; Coverage: 34%)
Gene names: Hnf6, Hnf6a, Onecut1
Sequence domains:
Structure domains:
5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: Rattus norvegicus
Expression system: Not provided
5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 14 nucleotides
Theoretical weight: 4.29 KDa
Source organism: Rattus norvegicus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ACT 2 x ACT
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: P2
Unit cell:
a: 73.02Å b: 38.958Å c: 106.5Å
α: 90° β: 107.63° γ: 90°
R-values:
R R work R free
0.247 0.245 0.269
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Homeodomain proteins: an update.
Bürglin et al. (2016)
3 more

6 mentions without citation

ONECUT2 is a targetable master regulator of lethal prostate cancer that suppresses the androgen axis.
Rotinen et al. (2018)
5 more