Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 27771.27 
• Atom Count: 1810 
• Residue Count: 244 
• Unique protein chains: 2

4K4J

Crystal structure of human Retinoid X Receptor alpha-ligand binding domain complex with 9cUAB30 and the coactivator peptide GRIP-1

• DOI: 10.2210/pdb4K4J/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-04-12 Released: 2013-11-13 
• Deposition Author(s): Xia, G., Smith, C.D., Muccio, D.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.283 
• R-Value Work: 0.240 

Literature

Defining the Communication between Agonist and Coactivator Binding in the Retinoid X Receptor alpha Ligand Binding Domain.

Boerma, L.J., Xia, G., Qui, C., Cox, B.D., Chalmers, M.J., Smith, C.D., Lobo-Ruppert, S., Griffin, P.R., Muccio, D.D., Renfrow, M.B.

(2014) J.Biol.Chem. 289: 814-826

• PubMed: 24187139 
• DOI: 10.1074/jbc.M113.476861
• Primary Citation of Related Structures:  
  4K6I


• PubMed Abstract: 
  

Retinoid X receptors (RXRs) are obligate partners for several other nuclear receptors, and they play a key role in several signaling processes. Despite being a promiscuous heterodimer partner, this nuclear receptor is a target of therapeutic intervention through activation using selective RXR agonists (rexinoids). Agonist binding to RXR initiates a large conformational change in the receptor that allows for coactivator recruitment to its surface and enhanced transcription. Here we reveal the structural and dynamical changes produced when a coactivator peptide binds to the human RXRα ligand binding domain containing two clinically relevant rexinoids, Targretin and 9-cis-UAB30. Our results show that the structural changes are very similar for each rexinoid and similar to those for the pan-agonist 9-cis-retinoic acid. The four structural changes involve key residues on helix 3, helix 4, and helix 11 that move from a solvent-exposed environment to one that interacts extensively with helix 12. Hydrogen-deuterium exchange mass spectrometry reveals that the dynamics of helices 3, 11, and 12 are significantly decreased when the two rexinoids are bound to the receptor. When the pan-agonist 9-cis-retinoic acid is bound to the receptor, only the dynamics of helices 3 and 11 are reduced. The four structural changes are conserved in all x-ray structures of the RXR ligand-binding domain in the presence of agonist and coactivator peptide. They serve as hallmarks for how RXR changes conformation and dynamics in the presence of agonist and coactivator to initiate signaling.

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Organizational Affiliation: 

From the Departments of Biochemistry and Molecular Genetics.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Retinoic acid receptor RXR-alpha	A	231	Homo sapiens	Mutation(s): 0  Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens) Go to Gene View: RXRA Go to UniProtKB:  P19793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nuclear receptor coactivator 2 peptide	B	13	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens) Go to Gene View: NCOA2 Go to UniProtKB:  Q15596

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
1O8	A	(2E,4E,6Z,8E)-8-(3,4-dihydronaphthalen-1(2H)-ylidene)-3,7-dimethylocta-2,4,6-trienoic acid C20 H22 O2 PPGNMFUMZSAZCW-VOYUZAMQSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
1O8	Kd: 33 - 1880 nM (100) BINDINGDB
1O8	EC50: 400 - 820 nM (99) BINDINGDB
1O8	Kd: 752 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.283 
• R-Value Work: 0.240 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 66.040	α = 90.00
b = 66.040	β = 90.00
c = 111.160	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-12 
• Released Date: 2013-11-13 
• Deposition Author(s): Xia, G., Smith, C.D., Muccio, D.D.

Revision History 

• Version 1.0: 2013-11-13
  Type: Initial release
• Version 1.1: 2013-12-11
  Type: Database references
• Version 1.2: 2014-01-29
  Type: Database references