Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37201.40 
• Atom Count: 2204 
• Residue Count: 256 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1KB4

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

• DOI: 10.2210/pdb1KB4/pdb
• NDB: PD0269

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2001-11-05 Released: 2002-05-03 
• Deposition Author(s): Shaffer, P.L., Gewirth, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.272 
• R-Value Work: 0.214 

Literature

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

Shaffer, P.L., Gewirth, D.T.

(2002) EMBO J. 21: 2242-2252

• PubMed: 11980721 
• DOI: 10.1093/emboj/21.9.2242
• Primary Citation of Related Structures:  
  1KB6, 1KB2


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Vitamin D3 Receptor	A, B	110	Homo sapiens	Mutation(s): 0  Gene Names: VDR (NR1I1)
Find proteins for P11473 (Homo sapiens) Go to Gene View: VDR Go to UniProtKB:  P11473

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*CP*AP*CP*AP*GP*GP*TP*CP*AP*CP*GP*AP*AP*GP*GP*TP*CP*A)-3'	C	18	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*TP*GP*AP*CP*CP*TP*TP*CP*GP*TP*GP*AP*CP*CP*TP*GP*TP*G)-3'	D	18	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.272 
• R-Value Work: 0.214 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 61.500	α = 90.00
b = 61.500	β = 90.00
c = 241.970	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-05 
• Released Date: 2002-05-03 
• Deposition Author(s): Shaffer, P.L., Gewirth, D.T.

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