4ZO1

Crystal Structure of the T3-bound TR-beta Ligand-binding Domain in complex with RXR-alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.221 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural mechanism for signal transduction in RXR nuclear receptor heterodimers.

Kojetin, D.J.Matta-Camacho, E.Hughes, T.S.Srinivasan, S.Nwachukwu, J.C.Cavett, V.Nowak, J.Chalmers, M.J.Marciano, D.P.Kamenecka, T.M.Shulman, A.I.Rance, M.Griffin, P.R.Bruning, J.B.Nettles, K.W.

(2015) Nat Commun 6: 8013-8013

  • DOI: 10.1038/ncomms9013

  • PubMed Abstract: 
  • A subset of nuclear receptors (NRs) function as obligate heterodimers with retinoid X receptor (RXR), allowing integration of ligand-dependent signals across the dimer interface via an unknown structural mechanism. Using nuclear magnetic resonance (N ...

    A subset of nuclear receptors (NRs) function as obligate heterodimers with retinoid X receptor (RXR), allowing integration of ligand-dependent signals across the dimer interface via an unknown structural mechanism. Using nuclear magnetic resonance (NMR) spectroscopy, x-ray crystallography and hydrogen/deuterium exchange (HDX) mass spectrometry, here we show an allosteric mechanism through which RXR co-operates with a permissive dimer partner, peroxisome proliferator-activated receptor (PPAR)-γ, while rendered generally unresponsive by a non-permissive dimer partner, thyroid hormone (TR) receptor. Amino acid residues that mediate this allosteric mechanism comprise an evolutionarily conserved network discovered by statistical coupling analysis (SCA). This SCA network acts as a signalling rheostat to integrate signals between dimer partners, ligands and coregulator-binding sites, thereby affecting signal transmission in RXR heterodimers. These findings define rules guiding how NRs integrate two ligand-dependent signalling pathways into RXR heterodimer-specific responses.


    Organizational Affiliation

    Department of Molecular Therapeutics, The Scripps Research Institute-Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thyroid hormone receptor beta
X
252Homo sapiensMutation(s): 0 
Gene Names: THRB (ERBA2, NR1A2, THR1)
Find proteins for P10828 (Homo sapiens)
Go to Gene View: THRB
Go to UniProtKB:  P10828
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
A
9Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Retinoic acid receptor RXR-alpha
B
225Homo sapiensMutation(s): 0 
Gene Names: RXRA (NR2B1)
Find proteins for P19793 (Homo sapiens)
Go to Gene View: RXRA
Go to UniProtKB:  P19793
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T3
Query on T3

Download SDF File 
Download CCD File 
X
3,5,3'TRIIODOTHYRONINE
T3; THYROID HORMONE; LIOTHYRONINE
C15 H12 I3 N O4
AUYYCJSJGJYCDS-LBPRGKRZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.221 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.236 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.252α = 90.00
b = 63.252β = 90.00
c = 225.806γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-09-02
    Type: Initial release