3UVV

Crystal Structure of the ligand binding domains of the thyroid receptor:retinoid X receptor complexed with 3,3',5 triiodo-L-thyronine and 9-cis retinoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for negative cooperativity within agonist-bound TR:RXR heterodimers.

Putcha, B.D.Wright, E.Brunzelle, J.S.Fernandez, E.J.

(2012) Proc Natl Acad Sci U S A 109: 6084-6087

  • DOI: 10.1073/pnas.1119852109
  • Primary Citation of Related Structures:  
    3UVV

  • PubMed Abstract: 
  • Thyroid hormones such as 3,3',5 triiodo-L-thyronine (T3) control numerous aspects of mammalian development and metabolism. The actions of such hormones are mediated by specific thyroid hormone receptors (TRs). TR belongs to the nuclear receptor famil ...

    Thyroid hormones such as 3,3',5 triiodo-L-thyronine (T3) control numerous aspects of mammalian development and metabolism. The actions of such hormones are mediated by specific thyroid hormone receptors (TRs). TR belongs to the nuclear receptor family of modular transcription factors that binds to specific DNA-response elements within target promoters. These receptors can function as homo- or heterodimers such as TR:9-cis retinoic acid receptor (RXR). Here, we present the atomic resolution structure of the TRα•T3:RXRα•9-cis retinoic acid (9c) ligand binding domain heterodimer complex at 2.95 Å along with T3 hormone binding and dissociation and coactivator binding studies. Our data provide a structural basis for allosteric communication between T3 and 9c and negative cooperativity between their binding pockets. In this structure, both TR and RXR are in the active state conformation for optimal binding to coactivator proteins. However, the structure of TR•T3 within TR•T3:RXR•9c is in a relative state of disorder, and the observed kinetics of binding show that T3 dissociates more rapidly from TR•T3:RXR•9c than from TR•T3:RXR. Also, coactivator binding studies with a steroid receptor coactivator-1 (receptor interaction domains 1-3) fragment show lower affinities (K(a)) for TR•T3:RXR•9c than TR•T3:RXR. Our study corroborates previously reported observations from cell-based and binding studies and offers a structural mechanism for the repression of TR•T3:RXR transactivation by RXR agonists. Furthermore, the recent discoveries of multiple endogenous RXR agonists that mediate physiological tasks such as lipid biosynthesis underscore the pharmacological importance of negative cooperativity in ligand binding within TR:RXR heterodimers.


    Organizational Affiliation

    University of Tennessee, Knoxville, TN 37996, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thyroid hormone receptor alphaA265Gallus gallusMutation(s): 0 
Gene Names: THRANR1A1
Find proteins for P04625 (Gallus gallus)
Explore P04625 
Go to UniProtKB:  P04625
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoic acid receptor RXR-alphaB244Homo sapiensMutation(s): 0 
Gene Names: RXRANR2B1
Find proteins for P19793 (Homo sapiens)
Explore P19793 
Go to UniProtKB:  P19793
NIH Common Fund Data Resources
PHAROS  P19793
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T3
Query on T3

Download CCD File 
A
3,5,3'TRIIODOTHYRONINE
C15 H12 I3 N O4
AUYYCJSJGJYCDS-LBPRGKRZSA-N
 Ligand Interaction
9CR
Query on 9CR

Download CCD File 
B
(9cis)-retinoic acid
C20 H28 O2
SHGAZHPCJJPHSC-ZVCIMWCZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9CRKd:  30   nM  BindingDB
9CRIC50:  29   nM  BindingDB
9CRKd:  3   nM  BindingDB
9CREC50:  4.5   nM  BindingDB
T3IC50:  3.200000047683716   nM  BindingDB
9CREC50:  124   nM  BindingDB
9CREC50:  120   nM  BindingDB
T3Kd:  0.17000000178813934   nM  BindingDB
9CRIC50:  12   nM  BindingDB
9CREC50:  29   nM  BindingDB
9CREC50:  2.5999999046325684   nM  BindingDB
9CRKi:  9   nM  BindingDB
9CRKd:  4   nM  BindingDB
9CREC50:  195   nM  BindingDB
9CRKd:  15   nM  BindingDB
9CRKd:  14   nM  BindingDB
9CRKd:  1560   nM  BindingDB
T3IC50:  0.23999999463558197   nM  BindingDB
9CRKi:  8.399999618530273   nM  BindingDB
9CRKd:  16   nM  BindingDB
9CRKd:  1810   nM  BindingDB
9CREC50:  250   nM  BindingDB
9CRKd:  8   nM  BindingDB
9CREC50:  316   nM  BindingDB
9CRKd:  9   nM  BindingDB
9CRKi:  12   nM  BindingDB
T3EC50:  2   nM  BindingDB
9CRKi:  3.799999952316284   nM  BindingDB
9CRKd:  12   nM  BindingDB
9CREC50:  1.5   nM  BindingDB
T3IC50:  500   nM  BindingDB
T3Ki:  0.2199999988079071   nM  BindingDB
9CRKd:  13   nM  BindingDB
9CRKi:  8   nM  BindingDB
9CRKd:  14   nM  BindingDB
T3Ki:  2.299999952316284   nM  BindingDB
T3EC50:  0.4099999964237213   nM  BindingDB
T3EC50:  11   nM  BindingDB
T3EC50:  2.0999999046325684   nM  BindingDB
T3Kd:  0.05999999865889549   nM  BindingDB
T3EC50:  15   nM  BindingDB
T3Kd:  0.09000000357627869   nM  BindingDB
T3Ki:  2.3299999237060547   nM  BindingDB
T3EC50:  2.4000000953674316   nM  BindingDB
9CRIC50:  32   nM  BindingDB
9CRKd:  32   nM  BindingDB
9CREC50:  6   nM  BindingDB
9CRKi:  27   nM  BindingDB
T3IC50:  1.7999999523162842   nM  BindingDB
T3EC50:  2   nM  BindingDB
9CRKd:  50   nM  BindingDB
9CRKd:  15   nM  BindingDB
T3EC50:  2.4000000953674316   nM  BindingDB
9CREC50:  200   nM  BindingDB
9CREC50:  120   nM  BindingDB
9CREC50:  10   nM  BindingDB
9CRKd:  11   nM  BindingDB
9CREC50:  110   nM  BindingDB
9CRKd:  35   nM  BindingDB
9CREC50:  13   nM  BindingDB
T3IC50:  2.9000000953674316   nM  BindingDB
9CRKi:  13   nM  BindingDB
T3Kd:  0.14000000059604645   nM  BindingDB
9CRKi:  11   nM  BindingDB
9CRIC50:  82   nM  BindingDB
T3Kd:  0.10000000149011612   nM  BindingDB
9CREC50:  4.300000190734863   nM  BindingDB
T3Ki:  0.07999999821186066   nM  BindingDB
9CRKi:  7.400000095367432   nM  BindingDB
9CRKi:  14   nM  BindingDB
T3Ki:  0.550000011920929   nM  BindingDB
9CRIC50:  4   nM  BindingDB
T3Kd:  0.07999999821186066   nM  BindingDB
9CRKd:  240   nM  BindingDB
9CREC50:  219   nM  BindingDB
9CREC50:  140   nM  BindingDB
9CRKd:  1.5   nM  BindingDB
T3Ki:  2.299999952316284   nM  BindingDB
9CREC50:  128   nM  BindingDB
T3Ki:  0.6800000071525574   nM  BindingDB
T3EC50:  10   nM  BindingDB
T3Ki:  0.33000001311302185   nM  BindingDB
9CREC50:  200   nM  BindingDB
T3Kd:  0.10000000149011612   nM  BindingDB
T3Ki:  2.2899999618530273   nM  BindingDB
T3IC50:  0.25999999046325684   nM  BindingDB
9CREC50:  100   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.13α = 90
b = 165.32β = 90
c = 85.1γ = 90
Software Package:
Software NamePurpose
AMoREphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-05-02
    Changes: Database references
  • Version 1.2: 2016-11-16
    Changes: Non-polymer description