1KB6

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

• PDB DOI:  https://doi.org/10.2210/pdb1KB6/pdb
• NAKB: 1KB6

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.223 

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: https://doi.org/10.1093/emboj/21.9.2242
• Primary Citation of Related Structures:  
  1KB2, 1KB4, 1KB6


• 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.2 kDa 
• Atom Count: 2,271 
• Modelled Residue Count: 231 
• Deposited Residue Count: 256 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 Receptor	C [auth A], D [auth B]	110	Homo sapiens	Mutation(s): 0  Gene Names: VDR, NR1I1
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens) Explore P11473  Go to UniProtKB:  P11473
PHAROS:  P11473

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.223 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.15	α = 90
b = 61.15	β = 90
c = 241.8	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description