1XZX

Thyroxine-Thyroid Hormone Receptor Interactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Thyroxine-thyroid hormone receptor interactions.

Sandler, B.Webb, P.Apriletti, J.W.Huber, B.R.Togashi, M.Cunha Lima, S.T.Juric, S.Nilsson, S.Wagner, R.Fletterick, R.J.Baxter, J.D.

(2004) J Biol Chem 279: 55801-55808

  • DOI: 10.1074/jbc.M410124200
  • Primary Citation of Related Structures:  
    1XZX, 1Y0X

  • PubMed Abstract: 
  • Thyroid hormone (TH) actions are mediated by nuclear receptors (TRs alpha and beta) that bind triiodothyronine (T(3), 3,5,3'-triiodo-l-thyronine) with high affinity, and its precursor thyroxine (T(4), 3,5,3',5'-tetraiodo-l-thyronine) with lower affin ...

    Thyroid hormone (TH) actions are mediated by nuclear receptors (TRs alpha and beta) that bind triiodothyronine (T(3), 3,5,3'-triiodo-l-thyronine) with high affinity, and its precursor thyroxine (T(4), 3,5,3',5'-tetraiodo-l-thyronine) with lower affinity. T(4) contains a bulky 5' iodine group absent from T(3). Because T(3) is buried in the core of the ligand binding domain (LBD), we have predicted that TH analogues with 5' substituents should fit poorly into the ligand binding pocket and perhaps behave as antagonists. We therefore examined how T(4) affects TR activity and conformation. We obtained several lines of evidence (ligand dissociation kinetics, migration on hydrophobic interaction columns, and non-denaturing gels) that TR-T(4) complexes adopt a conformation that differs from TR-T(3) complexes in solution. Nonetheless, T(4) behaves as an agonist in vitro (in effects on coregulator and DNA binding) and in cells, when conversion to T(3) does not contribute to agonist activity. We determined x-ray crystal structures of the TRbeta LBD in complex with T(3) and T(4) at 2.5-A and 3.1-A resolution. Comparison of the structures reveals that TRbeta accommodates T(4) through subtle alterations in the loop connecting helices 11 and 12 and amino acid side chains in the pocket, which, together, enlarge a niche that permits helix 12 to pack over the 5' iodine and complete the coactivator binding surface. While T(3) is the major active TH, our results suggest that T(4) could activate nuclear TRs at appropriate concentrations. The ability of TR to adapt to the 5' extension should be considered in TR ligand design.


    Organizational Affiliation

    Metabolic Research Unit and Diabetes Center, School of Medicine, University of California-San Francisco, 513 Parnassus Avenue, San Francisco, CA 94122-0540, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thyroid hormone receptor beta-1X281Homo sapiensMutation(s): 0 
Gene Names: THRBERBA2NR1A2THR1
Find proteins for P10828 (Homo sapiens)
Explore P10828 
Go to UniProtKB:  P10828
NIH Common Fund Data Resources
PHAROS  P10828
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T3
Query on T3

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

Download CCD File 
X
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T3EC50:  15   nM  BindingDB
T3Kd:  0.09000000357627869   nM  BindingDB
T3EC50:  2.4000000953674316   nM  BindingDB
T3Ki:  0.6800000071525574   nM  BindingDB
T3Ki:  2.2899999618530273   nM  BindingDB
T3IC50:  500   nM  BindingDB
T3Ki:  2.299999952316284   nM  BindingDB
T3Kd:  0.14000000059604645   nM  BindingDB
T3Kd:  0.07999999821186066   nM  BindingDB
T3EC50:  11   nM  BindingDB
T3Ki:  0.07999999821186066   nM  BindingDB
T3IC50:  0.25999999046325684   nM  BindingDB
T3Kd:  0.10000000149011612   nM  BindingDB
T3EC50:  2   nM  BindingDB
T3Ki:  0.550000011920929   nM  BindingDB
T3IC50:  1.7999999523162842   nM  BindingDB
T3Kd:  0.05999999865889549   nM  Binding MOAD
T3IC50:  2.9000000953674316   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.764α = 90
b = 68.764β = 90
c = 130.943γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description