› 3w5t

X-ray diffraction
2.29Å resolution

Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives

Released:
DOI: 10.2210/pdb3w5t/pdb
PDB entry 3w5t coloured by chain, front view.
PDB entry 3w5t coloured by chain, side view.
PDB entry 3w5t coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.
Masuno H, Ikura T, Morizono D, Orita I, Yamada S, Shimizu M, Ito N
J Lipid Res 54 2206-2213 (2013)
PMID: 23723390

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146463 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Vitamin D3 receptor Chain: A
Molecule details ›
Chain: A
Length: 271 amino acids
Theoretical weight: 30.6 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P13053 (Residues: 116-423; Coverage: 62%)
Gene names: Nr1i1, Vdr
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor
Mediator of RNA polymerase II transcription subunit 1 Chain: C
Molecule details ›
Chain: C
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15648 (Residues: 640-652; Coverage: 1%)
Gene names: ARC205, CRSP1, CRSP200, DRIP205, DRIP230, MED1, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2

Ligands and Environments

1 bound ligand:
Ligand LHP 1 x LHP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: C2
Unit cell:
a: 154.485Å b: 41.791Å c: 41.63Å
α: 90° β: 96.32° γ: 90°
R-values:
R R work R free
0.211 0.211 0.265
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

Endogenously produced nonclassical vitamin D hydroxy-metabolites act as "biased" agonists on VDR and inverse agonists on RORĪ± and RORĪ³.
Slominski et al. (2017)
12 more

3 mentions without citation

Crystal structures of complexes of vitamin D receptor ligand-binding domain with lithocholic acid derivatives.
Masuno et al. (2013)
2 more