1KB6

Crystal Structure of VDR DNA-binding Domain Bound to Rat Osteocalcin (OC) Response Element


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of VDR-DNA interactions on direct repeat response elements.

Shaffer, P.L.Gewirth, D.T.

(2002) EMBO J. 21: 2242-2252

  • DOI: 10.1093/emboj/21.9.2242
  • Primary Citation of Related Structures:  1KB2, 1KB4

  • PubMed Abstract: 
  • The vitamin D receptor (VDR) forms homo- or heterodimers on response elements composed of two hexameric half-sites separated by 3 bp of spacer DNA. We describe here the crystal structures at 2.7-2.8 A resolution of the VDR DNA-binding region (DBD) in ...

    The vitamin D receptor (VDR) forms homo- or heterodimers on response elements composed of two hexameric half-sites separated by 3 bp of spacer DNA. We describe here the crystal structures at 2.7-2.8 A resolution of the VDR DNA-binding region (DBD) in complex with response elements from three different promoters: osteopontin (SPP), canonical DR3 and osteocalcin (OC). These structures reveal the chemical basis for the increased affinity of VDR for the SPP response element, and for the poor stability of the VDR-OC complex, relative to the canonical DR3 response element. The homodimeric protein-protein interface is stabilized by van der Waals interactions and is predominantly non-polar. An extensive alpha-helix at the C-terminal end of the VDR DBD resembles that found in the thyroid hormone receptor (TR), and suggests a mechanism by which VDR and TR discriminate among response elements. Selective structure-based mutations in the asymmetric homodimeric interface result in a VDR DBD protein that is defective in homodimerization but now forms heterodimers with the 9-cis retinoic acid receptor (RXR) DBD.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 Receptor
A, B
110Homo sapiensGene Names: VDR (NR1I1)
Find proteins for P11473 (Homo sapiens)
Go to Gene View: VDR
Go to UniProtKB:  P11473
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*AP*CP*GP*GP*GP*TP*GP*AP*AP*TP*GP*AP*GP*GP*AP*CP*A)-3'C18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*GP*TP*CP*CP*TP*CP*AP*TP*TP*CP*AP*CP*CP*CP*GP*TP*G)-3'D18N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.223 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.150α = 90.00
b = 61.150β = 90.00
c = 241.800γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance