Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29152.88 
• Atom Count: 2041 
• Residue Count: 253 
• Unique protein chains: 1

3M7R

Crystal structure of VDR H305Q mutant

• DOI: 10.2210/pdb3M7R/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2010-03-17 Released: 2010-05-05 
• Deposition Author(s): Rochel, N., Hourai, S., Moras, D., Structural Proteomics in Europe (SPINE)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.241 
• R-Value Work: 0.211 

Literature

Crystal structure of hereditary vitamin D-resistant rickets--associated mutant H305Q of vitamin D nuclear receptor bound to its natural ligand

Rochel, N., Hourai, S., Moras, D.

(2010) J.Steroid Biochem.Mol.Biol. 121: 84-87

• PubMed: 20403435 
• DOI: 10.1016/j.jsbmb.2010.04.008


• PubMed Abstract: 
  

In the nuclear receptor of vitamin D (VDR) histidine 305 participates to the anchoring of the ligand. The VDR H305Q mutation was identified in a patient who exhibited the hereditary vitamin D-resistant rickets (HVDRR). We report the crystal structure of human VDR H305Q-ligand binding domain bound to 1alpha,25(OH)2D3 solved at 1.8A resolution. The protein adopts the active conformation of the wild-type liganded VDR. A local conformational flexibility at the mutation site weakens the hydrogen bond between the 25-OH with Gln305, thus explaining the lower affinity of the mutant proteins for calcitriol. The structure provides the basis for a rational approach to the design of more potent ligands for the treatment of HVDRR.

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Organizational Affiliation: 

IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie et de Génomique Structurales, Centre National de la Recherche Scientifique, Institut National de la Santé de la Recherche Médicale, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Vitamin D3 receptor	A	253	Homo sapiens	Mutation(s): 1  Gene Names: VDR (NR1I1)
Find proteins for P11473 (Homo sapiens) Go to Gene View: VDR Go to UniProtKB:  P11473

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
VDX	A	5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL 1,25 DIHYDROXY VITAMIN D3 C27 H44 O3 GMRQFYUYWCNGIN-NKMMMXOESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.241 
• R-Value Work: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 44.402	α = 90.00
b = 51.670	β = 90.00
c = 131.888	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-17 
• Released Date: 2010-05-05 
• Deposition Author(s): Rochel, N., Hourai, S., Moras, D., Structural Proteomics in Europe (SPINE)

Revision History 

• Version 1.0: 2010-05-05
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2014-02-19
  Type: Database references
• Version 1.3: 2018-02-07
  Type: Advisory, Experimental preparation