PDBsum entry 1ynw

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protein dna_rna metals links
Transcription/DNA PDB id
Protein chains
96 a.a. *
73 a.a. *
_ZN ×4
* Residue conservation analysis
PDB id:
Name: Transcription/DNA
Title: Crystal structure of vitamin d receptor and 9-cis retinoic a receptor DNA-binding domains bound to a dr3 response elemen
Structure: 5'-d( Tp Tp Ap Gp Gp Tp Cp Ap Cp Gp Ap Ap Gp Gp T -3'. Chain: c. Engineered: yes. Other_details: dr3 response element. 5'-d( Tp Tp Tp Gp Ap Cp Cp Tp Tp Cp Gp Tp Gp Ap C -3'. Chain: d. Engineered: yes.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: vdr, nr1i1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: rxra, nr2b1.
Biol. unit: Tetramer (from PQS)
3.00Å     R-factor:   0.232     R-free:   0.283
Authors: P.L.Shaffer,D.T.Gewirth
Key ref: P.L.Shaffer and D.T.Gewirth (2004). Structural analysis of RXR-VDR interactions on DR3 DNA. J Steroid Biochem Mol Biol, 89, 215-219. PubMed id: 15225774 DOI: 10.1016/j.jsbmb.2004.03.084
25-Jan-05     Release date:   15-Feb-05    
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Protein chain
Pfam   ArchSchema ?
P11473  (VDR_HUMAN) -  Vitamin D3 receptor
427 a.a.
96 a.a.*
Protein chain
Pfam   ArchSchema ?
P19793  (RXRA_HUMAN) -  Retinoic acid receptor RXR-alpha
462 a.a.
73 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     6 terms  


DOI no: 10.1016/j.jsbmb.2004.03.084 J Steroid Biochem Mol Biol 89:215-219 (2004)
PubMed id: 15225774  
Structural analysis of RXR-VDR interactions on DR3 DNA.
P.L.Shaffer, D.T.Gewirth.
The Vitamin D receptor (VDR) is a ligand-responsive transcription factor that forms homo- or heterodimers on response elements composed of two hexameric half-sites separated by three base pairs of spacer DNA. Binding of 1alpha,25-dihydroxyvitamin D(3) to the full-length VDR causes destabilization of the VDR homodimer and formation of a heterodimeric complex with the 9-cis retinoic acid receptor (RXR). VDR and RXR DNA-binding domains (DBDs) do not mimic this behavior, however: VDR DBD homodimers are formed exclusively, even in the presence of excess RXR DBD. Exploiting the asymmetry of the heterodimer and our knowledge of the homodimeric DBD interface, we have engineered VDR mutants that disfavor the homodimeric complex and allow for the formation of heterodimeric DBD complexes with RXR on DR3 elements. One of these complexes has been crystallized and its structure determined. However, the polarity of the proteins relative to the DNA is non-physiological due to crystal packing between symmetry-related VDR DBD protomers. This reveals a flattened energy landscape that appears to rely on elements outside of the core DBD for response element discrimination in the heterodimer.

Literature references that cite this PDB file's key reference

  PubMed id Reference
16204233 R.Yasmin, R.M.Williams, M.Xu, and N.Noy (2005).
Nuclear import of the retinoid X receptor, the vitamin D receptor, and their mutual heterodimer.
  J Biol Chem, 280, 40152-40160.  
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