› 1kb4

X-ray diffraction
2.8Å resolution

Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element

Released:
DOI: 10.2210/pdb1kb4/pdb
PDB entry 1kb4 coloured by chain, front view.
PDB entry 1kb4 coloured by chain, side view.
PDB entry 1kb4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of VDR-DNA interactions on direct repeat response elements.
Shaffer PL, Gewirth DT
EMBO J 21 2242-52 (2002)
PMID: 11980721

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-114070 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Vitamin D3 receptor Chains: A, B
Molecule details ›
Chains: A, B
Length: 110 amino acids
Theoretical weight: 12.95 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
5'-D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 18 nucleotides
Theoretical weight: 5.53 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*GP*TP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 18 nucleotides
Theoretical weight: 5.5 KDa
Source organism: Homo sapiens
Expression system: Not provided

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 19-BM
Spacegroup: P43212
Unit cell:
a: 61.5Å b: 61.5Å c: 241.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.214 0.272
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

21 review citations

Vitamin D.
Dusso et al. (2005)
20 more

9 mentions without citation

The nuclear receptor superfamily: A structural perspective.
Weikum et al. (2018)
8 more