Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 36.35 kDa 
• Atom Count: 2086 
• Modelled Residue Count: 235 
• Deposited Residue Count: 308 
• Unique protein chains: 2

3IPQ

X-ray structure of GW3965 synthetic agonist bound to the LXR-alpha

• PDB DOI: 10.2210/pdb3IPQ/pdb

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


• Deposited: 2009-08-18 Released: 2010-06-02 
• Deposition Author(s): Fradera, X., Vu, D., Nimz, O., Skene, R., Hosfield, D., Wijnands, R., Cooke, A.J., Haunso, A., King, A., Bennet, D.J., McGuire, R., Uitdehaag, J.C.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

X-ray structures of the LXRalpha LBD in its homodimeric form and implications for heterodimer signaling.

Fradera, X., Vu, D., Nimz, O., Skene, R., Hosfield, D., Wynands, R., Cooke, A.J., Haunso, A., King, A., Bennett, D.J., McGuire, R., Uitdehaag, J.C.

(2010) J Mol Biol 399: 120-132

• PubMed: 20382159 
• DOI: 10.1016/j.jmb.2010.04.005
• Primary Citation of Related Structures:  
  3IPQ, 3IPS, 3IPU


• PubMed Abstract: 
  

Liver X receptors (LXRs) are nuclear receptors that are central regulators of cholesterol homeostasis, and synthetic LXR agonists have shown promise as promoters of reverse cholesterol transport and anti-inflammatory agents. Here, we present three X-ray structures of three different agonists bound to the ligand binding domain of LXRalpha. These compounds are GW3965, F(3)methylAA, and a benzisoxazole urea, and we show that these diverse chemical scaffolds address common structural themes, leading to high binding affinity for LXR. Our structures show the LXRalpha ligand binding domain in its homodimeric form, an arrangement previously thought to be stereochemically difficult. A comparison with existing structures of the LXRbeta homodimer and LXRalpha:RXR (retinoid X receptor) heterodimers explains differences in dimer affinity and leads us to propose a model for allosteric activation in nuclear receptor dimers, in which an unactivated RXR partner provides an inhibitory tail wrap to the cofactor binding pocket of LXR.

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Organizational Affiliation: 

Department of Chemistry, Merck Research Labs, Newhouse, ML1 5SH, Scotland, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxysterols receptor LXR-alpha	A	283	Homo sapiens	Mutation(s): 0  Gene Names: LXRA, NR1H3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13133 (Homo sapiens) Explore Q13133  Go to UniProtKB:  Q13133
PHAROS:  Q13133 GTEx:  ENSG00000025434

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	B	25	N/A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
965	C [auth A]	[3-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2-diphenylethyl)amino}propoxy)phenyl]acetic acid C33 H31 Cl F3 N O3 NAXSRXHZFIBFMI-UHFFFAOYSA-N
SO4	D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
965	PDBBind:  3IPQ	Ki: 27 (nM) from 1 assay(s)
	Binding MOAD:  3IPQ	Ki: 27 (nM) from 1 assay(s)
	BindingDB:  3IPQ	IC50: min: 100, max: 235 (nM) from 3 assay(s)
		EC50: min: 22, max: 1300 (nM) from 13 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.593	α = 90
b = 125.593	β = 90
c = 92.405	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-18 
• Released Date: 2010-06-02 
Deposition Author(s): Fradera, X., Vu, D., Nimz, O., Skene, R., Hosfield, D., Wijnands, R., Cooke, A.J., Haunso, A., King, A., Bennet, D.J., McGuire, R., Uitdehaag, J.C.M.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance