› 2zmi

X-ray diffraction
1.7Å resolution

Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism

Released:
DOI: 10.2210/pdb2zmi/pdb
PDB entry 2zmi coloured by chain, front view.
PDB entry 2zmi coloured by chain, side view.
PDB entry 2zmi coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of rat vitamin D receptor bound to adamantyl vitamin D analogs: structural basis for vitamin D receptor antagonism and partial agonism.
Nakabayashi M, Yamada S, Yoshimoto N, Tanaka T, Igarashi M, Ikura T, Ito N, Makishima M, Tokiwa H, DeLuca HF, Shimizu M
J Med Chem 51 5320-9 (2008)
PMID: 18710208

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106654 (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: Xenopus tropicalis
Expression system: Not provided
UniProt:
  • Canonical: A1L0Z0 (Residues: 624-636; Coverage: 1%)
Gene name: med1

Ligands and Environments

3 bound ligands:
Ligand TT2 1 x TT2
Ligand EDO 1 x EDO
Ligand FMT 1 x FMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2
Unit cell:
a: 155.222Å b: 42.412Å c: 41.955Å
α: 90° β: 95.21° γ: 90°
R-values:
R R work R free
0.212 0.212 0.222
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

A structural perspective on Mediator function.
Larivière et al. (2012)
8 more

2 mentions without citation

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