4K6I

Crystal structure of human retinoid X receptor alpha-ligand binding domain complex with Targretin and the coactivator peptide GRIP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1074/jbc.M113.476861
  • Primary Citation of Related Structures:  

  • 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 interven ...

    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.


    Organizational Affiliation

    From the Departments of Biochemistry and Molecular Genetics.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
A
231Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
B
13Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9RA
Query on 9RA

Download SDF File 
Download CCD File 
A
4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)ethenyl]benzoic acid
C24 H28 O2
NAVMQTYZDKMPEU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.246 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.150α = 90.00
b = 68.150β = 90.00
c = 106.590γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSphasing
HKL-2000data collection
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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
  • Version 1.3: 2018-04-04
    Type: Data collection