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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 se ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thyroid hormone receptor beta-1 A253Homo sapiensMutation(s): 0 
Gene Names: THRB OR NR1A2 OR ERBA2 OR THR1, THRB, ERBA2, NR1A2, THR1
Find proteins for P10828 (Homo sapiens)
Explore P10828 
Go to UniProtKB:  P10828
NIH Common Fund Data Resources
PHAROS:  P10828
GTEx:  ENSG00000151090
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G24
Query on G24
Download Ideal Coordinates CCD File 
A
[4-(3-BENZYL-4-HYDROXYBENZYL)-3,5-DIMETHYLPHENOXY]ACETIC ACID
C24 H24 O4
JYHIGYLGYNCMGI-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G24Kd :  0.33000001311302185   nM  PDBBind
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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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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