Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 27.77 kDa 
• Atom Count: 1925 
• Residue Count: 225 
• 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
• Mutation(s): No 


• 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: 2.00 Å
• R-Value Free: 0.283 
• R-Value Work: 0.240 
• R-Value Observed: 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:  
  4K4J, 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A	231	Homo sapiens	Mutation(s): 0  Gene Names: NR2B1, RXRA, RXRA NR2B1
Find proteins for P19793 (Homo sapiens) Explore P19793  Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS  P19793 GTEx  ENSG00000186350

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2 peptide	B	13	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2, BHLHE75, SRC2, TIF2
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS  Q15596 GTEx  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
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:  1880   nM  BindingDB
1O8	Kd:  33   nM  BindingDB
1O8	EC50:  400   nM  BindingDB
1O8	EC50:  820   nM  BindingDB
1O8	Kd:  1330   nM  BindingDB
1O8	EC50:  820   nM  BindingDB
1O8	Kd :  752   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.283 
• R-Value Work: 0.240 
• R-Value Observed: 0.240 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.04	α = 90
b = 66.04	β = 90
c = 111.16	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
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
  Changes: Database references
• Version 1.2: 2014-01-29
  Changes: Database references