Biological Assembly 1  

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Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 101130.23 
• Atom Count: 6334 
• Residue Count: 896 
• Unique protein chains: 1

1H9U

The structure of the human retinoid-X-receptor beta ligand binding domain in complex with the specific synthetic agonist LG100268

• DOI: 10.2210/pdb1H9U/pdb

• Classification: NUCLEAR RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2001-03-21 Released: 2002-04-03 
• Deposition Author(s): Schwabe, J.W.R., Love, J.D., Gooch, J.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.306 
• R-Value Work: 0.273 

Literature

The Structural Basis for the Specificity of Retinoid-X Receptor-Selective Agonists: New Insights Into the Role of Helix H12

Love, J.D., Gooch, J.T., Benko, S., Li, C., Nagy, L., Chatterjee, V.K.K., Evans, R.M., Schwabe, J.W.R.

(2002) J.Biol.Chem. 277: 11385

• PubMed: 11782480 
• DOI: 10.1074/jbc.M110869200


• PubMed Abstract: 
  

Ligands that specifically target retinoid-X receptors (RXRs) are emerging as potentially powerful therapies for cancer, diabetes, and the lowering of circulatory cholesterol. To date, RXR has only been crystallized in the absence of ligand or with the promiscuous ligand 9-cis retinoic acid, which also activates retinoic acid receptors. Here we present the structure of hRXRbeta in complex with the RXR-specific agonist LG100268 (LG268). The structure clearly reveals why LG268 is specific for the RXR ligand binding pocket and will not activate retinoic acid receptors. Intriguingly, in the crystals, the C-terminal "activation" helix (AF-2/helix H12) is trapped in a novel position not seen in other nuclear receptor structures such that it does not cap the ligand binding cavity. Mammalian two-hybrid assays indicate that LG268 is unable to release co-repressors from RXR unless co-activators are also present. Together these findings suggest that RXR ligands may be inefficient at repositioning helix H12.

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Organizational Affiliation: 

Medical Research Council, Laboratory of Molecular Biology, Cambridge, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RETINOID X RECEPTOR, BETA	A, B, C, D	224	Homo sapiens	Mutation(s): 0  Gene Names: RXRB (NR2B2)
Find proteins for P28702 (Homo sapiens) Go to Gene View: RXRB Go to UniProtKB:  P28702

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NI	A, B, C, D	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
LG2	A, B, C, D	6-[1-(3,5,5,8,8-PENTAMETHYL-5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)CYCLOPROPYL]PYRIDINE-3-CARBOXYLIC ACID C24 H29 N O2 SLXTWXQUEZSSTJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LG2	EC50: 3 - 40 nM (98) BINDINGDB
LG2	Ki: 3 - 3515 nM (88) BINDINGDB
LG2	Kd: 3 nM (88) BINDINGDB
LG2	IC50: 0 nM (88) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.306 
• R-Value Work: 0.273 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 123.886	α = 90.00
b = 106.882	β = 122.56
c = 100.587	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALA	data scaling
CNS	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-03-21 
• Released Date: 2002-04-03 
• Deposition Author(s): Schwabe, J.W.R., Love, J.D., Gooch, J.T.

Revision History 

• Version 1.0: 2002-04-03
  Type: Initial release
• Version 1.1: 2011-05-07
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance