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: 3.22 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

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Ligand Structure Quality Assessment 


This is version 2.0 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: https://doi.org/10.1038/ncomms9013
  • Primary Citation of Related Structures:  
    4ZO1

  • 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 (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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thyroid hormone receptor betaA [auth X]252Homo sapiensMutation(s): 0 
Gene Names: THRBERBA2NR1A2THR1
UniProt & NIH Common Fund Data Resources
Find proteins for P10828 (Homo sapiens)
Explore P10828 
Go to UniProtKB:  P10828
PHAROS:  P10828
GTEx:  ENSG00000151090 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10828
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2B [auth A]9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
UniProt GroupQ15596
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaC [auth B]225Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
PHAROS:  P19793
GTEx:  ENSG00000186350 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19793
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T3
Query on T3

Download Ideal Coordinates CCD File 
D [auth X]3,5,3'TRIIODOTHYRONINE
C15 H12 I3 N O4
AUYYCJSJGJYCDS-LBPRGKRZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
T3 BindingDB:  4ZO1 Ki: min: 0.08, max: 2.3 (nM) from 5 assay(s)
Kd: min: 0.08, max: 0.14 (nM) from 4 assay(s)
IC50: min: 0.26, max: 500 (nM) from 5 assay(s)
EC50: min: 1.1, max: 35 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.22 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.252α = 90
b = 63.252β = 90
c = 225.806γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations