Crystal Structure Of The Nuclear Receptor For Vitamin D Ligand Binding Domain Bound to MC1288

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 

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Crystal structures of the vitamin D receptor complexed to superagonist 20-epi ligands.

Tocchini-Valentini, G.Rochel, N.Wurtz, J.M.Mitschler, A.Moras, D.

(2001) Proc Natl Acad Sci U S A 98: 5491-5496

  • DOI: https://doi.org/10.1073/pnas.091018698
  • Primary Citation of Related Structures:  
    1IE8, 1IE9

  • PubMed Abstract: 

    The crystal structures of the ligand-binding domain (LBD) of the vitamin D receptor complexed to 1alpha,25(OH)(2)D(3) and the 20-epi analogs, MC1288 and KH1060, show that the protein conformation is identical, conferring a general character to the observation first made for retinoic acid receptor (RAR) that, for a given LBD, the agonist conformation is unique, the ligands adapting to the binding pocket. In all complexes, the A- to D-ring moieties of the ligands adopt the same conformation and form identical contacts with the protein. Differences are observed only for the 17beta-aliphatic chains that adapt their conformation to anchor the 25-hydroxyl group to His-305 and His-397. The inverted geometry of the C20 methyl group induces different paths of the aliphatic chains. The ligands exhibit a low-energy conformation for MC1288 and a more strained conformation for the two others. KH1060 compensates this energy cost by additional contacts. Based on the present data, the explanation of the superagonist effect is to be found in higher stability and longer half-life of the active complex, thereby excluding different conformations of the ligand binding domain.

  • Organizational Affiliation

    Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université Louis Pasteur, France.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VITAMIN D3 RECEPTOR259Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens)
Explore P11473 
Go to UniProtKB:  P11473
PHAROS:  P11473
GTEx:  ENSG00000111424 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11473
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on VDX

Download Ideal Coordinates CCD File 
C27 H44 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
VDX PDBBind:  1IE9 Kd: 0.06 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.94α = 90
b = 51.42β = 90
c = 132.52γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-16
    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: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations