Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.76 kDa 
• Atom Count: 3692 
• Modelled Residue Count: 451 
• Deposited Residue Count: 498 
• Unique protein chains: 2

3OZJ

Crystal structure of human retinoic X receptor alpha complexed with bigelovin and coactivator SRC-1

• PDB DOI: 10.2210/pdb3OZJ/pdb

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


• Deposited: 2010-09-25 Released: 2011-02-02 
• Deposition Author(s): Zhang, H., Li, L., Chen, L., Hu, L., Shen, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.245 
• R-Value Observed: 0.245 

Literature

Structure basis of bigelovin as a selective RXR agonist with a distinct binding mode

Zhang, H., Li, L., Chen, L., Hu, L., Jiang, H., Shen, X.

(2011) J Mol Biol 407: 13-20

• PubMed: 21262235 
• DOI: 10.1016/j.jmb.2011.01.032
• Primary Citation of Related Structures:  
  3OZJ


• PubMed Abstract: 
  

The nuclear receptor retinoid X receptor (RXR) functions potently in the regulation of homeostasis and cell development, while rexinoids as RXR agonists have proved their therapeutic potential in the treatment of metabolic diseases and cancer. Here, the natural product bigelovin was identified as a selective RXRα agonist. Interestingly, this compound could not transactivate RXRα:RXRα homodimer but could enhance the transactivation of RXRα:peroxisome proliferator-activated receptor γ heterodimer and repress that of RXRα:liver X receptor (LXR) α heterodimer, while it had no effects on RXRα:farnesoid X receptor heterodimer. Considering that the effective role of LXR response element involved transactivation of sterol regulatory element-binding protein-1c mediated by RXRα:LXRα in triglyceride elevation, such LXR response element repressing by bigelovin has obviously addressed its potency for further research. Moreover, our determined crystal structure of the bigelovin-activated RXRα ligand-binding domain with the coactivator human steroid receptor coactivator-1 peptide revealed that bigelovin adopted a distinct binding mode. Compared with the known RXR ligands, bigelovin lacks the acidic moiety in structure, which indicated that the acidic moiety rendered little effects on RXR activation. Our results have thereby provided new insights into the structure-based selective rexinoids design with bigelovin as a potential lead compound.

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Organizational Affiliation: 

State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A, C	238	Homo sapiens	Mutation(s): 0  Gene Names: RXRA, NR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens) Explore P19793  Go to UniProtKB:  P19793
PHAROS:  P19793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SRC-1, peptide of Nuclear receptor coactivator 2	B, D	11	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2, BHLHE75, SRC2, TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGV	E [auth A], F [auth C]	(3aR,4S,4aR,7aR,8R,9aS)-4a,8-dimethyl-3-methylidene-2,5-dioxo-2,3,3a,4,4a,5,7a,8,9,9a-decahydroazuleno[6,5-b]furan-4-yl acetate C17 H20 O5 DCNRYQODUSSOKC-MMLVVLEOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BGV	PDBBind:  3OZJ	Kd: 7700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.245 
• R-Value Observed: 0.245 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.4	α = 90
b = 66.59	β = 90
c = 111.73	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-25 
• Released Date: 2011-02-02 
Deposition Author(s): Zhang, H., Li, L., Chen, L., Hu, L., Shen, X.

Revision History  

• Version 1.0: 2011-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-18
  Changes: Database references