› 1ynw

X-ray diffraction
3Å resolution

Crystal Structure of Vitamin D Receptor and 9-cis Retinoic Acid Receptor DNA-Binding Domains Bound to a DR3 Response Element

Released:
DOI: 10.2210/pdb1ynw/pdb
PDB entry 1ynw coloured by chain, front view.
PDB entry 1ynw coloured by chain, side view.
PDB entry 1ynw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of RXR-VDR interactions on DR3 DNA.
Shaffer PL, Gewirth DT
J Steroid Biochem Mol Biol 89-90 215-9 (2004)
PMID: 15225774

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114864 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Vitamin D3 receptor Chain: A
Molecule details ›
Chain: A
Length: 110 amino acids
Theoretical weight: 12.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11473 (Residues: 16-125; Coverage: 26%)
Gene names: NR1I1, VDR
Sequence domains: Zinc finger, C4 type (two domains)
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
Retinoic acid receptor RXR-alpha Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P19793 (Residues: 130-228; Coverage: 21%)
Gene names: NR2B1, RXRA
Sequence domains: Zinc finger, C4 type (two domains)
Structure domains: Erythroid Transcription Factor GATA-1, subunit A
5'-d(*TP*TP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*AP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.56 KDa
5'-d(*TP*TP*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*A)-3' Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.46 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-ID-B
Spacegroup: C2
Unit cell:
a: 123.104Å b: 57.049Å c: 73.438Å
α: 90° β: 110.31° γ: 90°
R-values:
R R work R free
0.232 0.232 0.283
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 review citations

Genome-wide (over)view on the actions of vitamin D.
Carlberg C. (2014)
10 more

10 mentions without citation

The retinoid X receptors and their ligands.
Dawson et al. (2012)
9 more