1Q4X

Crystal Structure of Human Thyroid Hormone Receptor beta LBD in complex with specific agonist GC-24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.228 

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This is version 1.3 of the entry. See complete history


Literature

Ligand selectivity by seeking hydrophobicity in thyroid hormone receptor.

Borngraeber, S.Budny, M.J.Chiellini, G.Cunha-Lima, S.T.Togashi, M.Webb, P.Baxter, J.D.Scanlan, T.S.Fletterick, R.J.

(2003) Proc Natl Acad Sci U S A 100: 15358-15363

  • DOI: https://doi.org/10.1073/pnas.2136689100
  • Primary Citation of Related Structures:  
    1Q4X

  • PubMed Abstract: 

    Selective therapeutics for nuclear receptors would revolutionize treatment for endocrine disease. Specific control of nuclear receptor activity is challenging because the internal cavities that bind hormones can be virtually identical. Only one highly selective hormone analog is known for the thyroid receptor, GC-24, an agonist for human thyroid hormone receptor beta. The compound differs from natural hormone in benzyl, substituting for an iodine atom in the 3' position. The benzyl is too large to fit into the enclosed pocket of the receptor. The crystal structure of human thyroid hormone receptor beta at 2.8-A resolution with GC-24 bound explains its agonist activity and unique isoform specificity. The benzyl of GC-24 is accommodated through shifts of 3-4 A in two helices. These helices are required for binding hormone and positioning the critical helix 12 at the C terminus. Despite these changes, the complex associates with coactivator as tightly as human thyroid hormone receptor bound to thyroid hormone and is fully active. Our data suggest that increased specificity of ligand recognition derives from creating a new hydrophobic cluster with ligand and protein components.


  • Organizational Affiliation

    Department of Biochemistry/Biophysics, University of California, San Francisco, CA 94143-2240, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thyroid hormone receptor beta-1253Homo sapiensMutation(s): 0 
Gene Names: THRB OR NR1A2 OR ERBA2 OR THR1
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G24
Query on G24

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
[4-(3-BENZYL-4-HYDROXYBENZYL)-3,5-DIMETHYLPHENOXY]ACETIC ACID
C24 H24 O4
JYHIGYLGYNCMGI-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
G24 PDBBind:  1Q4X Kd: 0.33 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.228 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.57α = 90
b = 56.57β = 90
c = 390.05γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations