› 3w0j

X-ray diffraction
1.84Å resolution

Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands

Released:
DOI: 10.2210/pdb3w0j/pdb
PDB entry 3w0j coloured by chain, front view.
PDB entry 3w0j coloured by chain, side view.
PDB entry 3w0j coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands.
Asano L, Ito I, Kuwabara N, Waku T, Yanagisawa J, Miyachi H, Shimizu T
FEBS Lett 587 957-63 (2013)
PMID: 23462137

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: 253 amino acids
Theoretical weight: 28.76 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P13053 (Residues: 121-420; Coverage: 60%)
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 T08 1 x T08
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: C2
Unit cell:
a: 154.214Å b: 42.39Å c: 42.144Å
α: 90° β: 94.89° γ: 90°
R-values:
R R work R free
0.225 0.223 0.259
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Vitamin D and Its Synthetic Analogs.
Maestro et al. (2019)
5 more

1 mention without citation

A multidisciplinary approach disclosing unexplored Aflatoxin B1 roles in severe impairment of vitamin D mechanisms of action.
Persico et al. (2023)