2HC4 | pdb_00002hc4

Crystal structure of the LBD of VDR of Danio rerio in complex with calcitriol

• PDB DOI: https://doi.org/10.2210/pdb2HC4/pdb

• Classification: GENE REGULATION
• Organism(s): Danio rerio, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-06-15 Released: 2007-05-01 
• Deposition Author(s): Ciesielski, F., Rochel, N., Moras, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Adaptability of the Vitamin D nuclear receptor to the synthetic ligand Gemini: remodelling the LBP with one side chain rotation

Ciesielski, F., Rochel, N., Moras, D.

(2007) J Steroid Biochem Mol Biol 103: 235-242

• PubMed: 17218092 
• DOI: https://doi.org/10.1016/j.jsbmb.2006.12.003
• Primary Citation of Related Structures:  
  2HC4, 2HCD


• PubMed Abstract: 
  

  The crystal structure of the ligand binding domain (LBD) of the wild-type Vitamin D receptor (VDR) of zebrafish bound to Gemini, a synthetic agonist ligand with two identical side chains branching at carbon 20 reveals a ligand-dependent structural rearrangement of the ligand binding pocket (LBP). The rotation of a Leu side chain opens the access to a channel that can accommodate the second side chain of the ligand. The 25% increase of the LBP's volume does not alter the essential agonist features of VDR. The possibility to adapt the LBP to novel ligands with different chemistry and/or structure opens new perspectives in the design of more specifically targeted ligands.

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Organizational Affiliation: 

Département de Biologie et de Génomique Structurales, IGBMC, CNRS/INSERM Université Louis Pasteur, Parc d'innovation BP10142, 67404 Illkirch Cedex, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 36.25 kDa 
• Atom Count: 2,119 
• Modelled Residue Count: 249 
• Deposited Residue Count: 317 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D receptor	A	302	Danio rerio	Mutation(s): 0
UniProt
Find proteins for Q9PTN2 (Danio rerio) Explore Q9PTN2  Go to UniProtKB:  Q9PTN2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SRC-1 from Nuclear receptor coactivator 1	B	15	Homo sapiens	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VDX	C [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	BindingDB:  2HC4	Kd: 1200 (nM) from 1 assay(s)
		EC50: 5.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.835	α = 90
b = 65.835	β = 90
c = 264.839	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Ciesielski, F., Rochel, N., Moras, D.

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-03-03
  Changes: Advisory, Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2023-10-25
  Changes: Advisory, Data collection, Database references, Refinement description