3GWS

Crystal Structure of T3-Bound Thyroid Hormone Receptor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thyroid hormone receptor beta X259Homo sapiensMutation(s): 0 
Gene Names: 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
T3
Query on T3
Download Ideal Coordinates CCD File 
X
3,5,3'TRIIODOTHYRONINE
C15 H12 I3 N O4
AUYYCJSJGJYCDS-LBPRGKRZSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS		XL-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T3Kd :  0.08100000023841858   nM  PDBBind
T3Kd:  0.07999999821186066   nM  BindingDB
T3Ki:  0.6800000071525574   nM  BindingDB
T3Kd:  0.09000000357627869   nM  BindingDB
T3EC50:  11   nM  BindingDB
T3Ki:  0.07999999821186066   nM  BindingDB
T3EC50:  2   nM  BindingDB
T3EC50:  2.4000000953674316   nM  BindingDB
T3Ki:  2.299999952316284   nM  BindingDB
T3Kd:  0.14000000059604645   nM  BindingDB
T3EC50:  1.4900000095367432   nM  BindingDB
T3IC50:  0.25999999046325684   nM  BindingDB
T3Ki:  2.2899999618530273   nM  BindingDB
T3IC50:  500   nM  BindingDB
T3Kd:  0.10000000149011612   nM  BindingDB
T3IC50:  1.7999999523162842   nM  BindingDB
T3IC50:  2.9000000953674316   nM  BindingDB
T3Ki:  0.550000011920929   nM  BindingDB
T3EC50:  15   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

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