2HBH | pdb_00002hbh

Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide

• PDB DOI: https://doi.org/10.2210/pdb2HBH/pdb

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


• Deposited: 2006-06-14 Released: 2007-05-01 
• Deposition Author(s): Rochel, N., Hourai, S., Moras, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the vitamin D nuclear receptor ligand binding domain in complex with a locked side chain analog of calcitriol

Rochel, N., Hourai, S., Perez-Garcia, X., Rumbo, A., Mourino, A., Moras, D.

(2007) Arch Biochem Biophys 460: 172-176

• PubMed: 17346665 
• DOI: https://doi.org/10.1016/j.abb.2007.01.031
• Primary Citation of Related Structures:  
  2HBH


• PubMed Abstract: 
  

  The crystal structures of vitamin D nuclear receptor (VDR) have revealed that all compounds are anchored by the same residues to the ligand binding pocket (LBP). Based on this observation, a synthetic analog with a locked side chain (21-nor-calcitriol-20(22),23-diyne) has been synthesized in order to gain in entropy energy with a predefined active side chain conformation. The crystal structure of VDR LBD bound to this locked side chain analogue while confirming the docking provides a structural basis for the activity of this compound.

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Organizational Affiliation: 

Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département de Biologie et de Génomique Structurales, Illkirch F-67400, 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: 36.23 kDa 
• Atom Count: 2,109 
• 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
XE4	C [auth A]	1,3-CYCLOHEXANEDIOL, 4-METHYLENE-5-[(2E)-[(1S,3AS,7AS)-OCTAHYDRO-1-(5-HYDROXY-5-METHYL-1,3-HEXADIYNYL)-7A-METHYL-4H-INDEN-4-YLIDENE]ETHYLIDENE]-, (1R,3S,5Z) C26 H34 O3 CEEUUHVULXTFGS-BQXVGYHGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.682	α = 90
b = 65.682	β = 90
c = 265.096	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): Rochel, N., Hourai, S., 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: Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description