1DB1

CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO VITAMIN D

• PDB DOI: https://doi.org/10.2210/pdb1DB1/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-11-02 Released: 2000-01-31 
• Deposition Author(s): Rochel, N., Wurtz, J.M., Mitschler, A., Klaholz, B., Moras, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.214 
• R-Value Work: 0.191 

Literature

The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand.

Rochel, N., Wurtz, J.M., Mitschler, A., Klaholz, B., Moras, D.

(2000) Mol Cell 5: 173-179

• PubMed: 10678179 
• DOI: https://doi.org/10.1016/s1097-2765(00)80413-x
• Primary Citation of Related Structures:  
  1DB1


• PubMed Abstract: 
  

  The action of 1 alpha, 25-dihydroxyvitamin D3 is mediated by its nuclear receptor (VDR), a ligand-dependent transcription regulator. We report the 1.8 A resolution crystal structure of the complex between a VDR ligand-binding domain (LBD) construct lacking the highly variable VDR-specific insertion domain and vitamin D. The construct exhibits the same binding affinity for vitamin D and transactivation ability as the wild-type protein, showing that the N-terminal part of the LBD is essential for its structural and functional integrity while the large insertion peptide is dispensable. The structure reveals the active conformation of the bound ligand and allows understanding of the different binding properties of some synthetic analogs.

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Organizational Affiliation: 

Laboratoire de Biologie Structurale, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/ULP, Illkirch, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.81 kDa 
• Atom Count: 2,186 
• Modelled Residue Count: 250 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VITAMIN D NUCLEAR RECEPTOR	A	259	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens) Explore P11473  Go to UniProtKB:  P11473
PHAROS:  P11473 GTEx:  ENSG00000111424

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
VDX	PDBBind:  1DB1	Kd: 0.55 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.214 
• R-Value Work: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.193	α = 90
b = 52.443	β = 90
c = 133.286	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-31 
Deposition Author(s): Rochel, N., Wurtz, J.M., Mitschler, A., Klaholz, B., Moras, D.

Revision History  

• Version 1.0: 2000-01-31
  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