Crystal Structure of T3-Bound Thyroid Hormone Receptor

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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Structural rearrangements in the thyroid hormone receptor hinge domain and their putative role in the receptor function

Nascimento, A.S.Dias, S.M.G.Nunes, F.M.Aparicio, R.Ambrosio, A.L.B.Bleicher, L.Figueira, A.C.M.Santos, M.A.M.de Oliveira Neto, M.Fischer, H.Togashi, M.Craievich, A.F.Garratt, R.C.Baxter, J.D.Webb, P.Polikarpov, I.

(2006) J Mol Biol 360: 586-598

  • DOI: https://doi.org/10.1016/j.jmb.2006.05.008
  • Primary Citation of Related Structures:  
    2H77, 2H79, 3GWS

  • PubMed Abstract: 

    The thyroid hormone receptor (TR) D-domain links the ligand-binding domain (LBD, EF-domain) to the DNA-binding domain (DBD, C-domain), but its structure, and even its existence as a functional unit, are controversial. The D domain is poorly conserved throughout the nuclear receptor family and was originally proposed to comprise an unfolded hinge that facilitates rotation between the LBD and the DBD. Previous TR LBD structures, however, have indicated that the true unstructured region is three to six amino acid residues long and that the D-domain N terminus folds into a short amphipathic alpha-helix (H0) contiguous with the DBD and that the C terminus of the D-domain comprises H1 and H2 of the LBD. Here, we solve structures of TR-LBDs in different crystal forms and show that the N terminus of the TRalpha D-domain can adopt two structures; it can either fold into an amphipathic helix that resembles TRbeta H0 or form an unstructured loop. H0 formation requires contacts with the AF-2 coactivator-binding groove of the neighboring TR LBD, which binds H0 sequences that resemble coactivator LXXLL motifs. Structural analysis of a liganded TR LBD with small angle X-ray scattering (SAXS) suggests that AF-2/H0 interactions mediate dimerization of this protein in solution. We propose that the TR D-domain has the potential to form functionally important extensions of the DBD and LBD or unfold to permit TRs to adapt to different DNA response elements. We also show that mutations of the D domain LXXLL-like motif indeed selectively inhibit TR interactions with an inverted palindromic response element (F2) in vitro and TR activity at this response element in cell-based transfection experiments.

  • Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense, 400 CEP 13560-970 São Carlos, SP, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thyroid hormone receptor betaA [auth X]259Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on T3

Download Ideal Coordinates CCD File 
C15 H12 I3 N O4
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CAS
Binding Affinity Annotations 
IDSourceBinding Affinity
T3 BindingDB:  3GWS 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: 1.49, max: 15 (nM) from 5 assay(s)
PDBBind:  3GWS Kd: 0.08 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.974α = 90
b = 68.974β = 90
c = 131.247γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection