2H77

Crystal structure of human TR alpha bound T3 in monoclinic space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.Neto, M.O.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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THRA protein
A
269Homo sapiensMutation(s): 1 
Gene Names: THRA (EAR7, ERBA1, NR1A1, THRA1, THRA2)
Find proteins for P10827 (Homo sapiens)
Go to Gene View: THRA
Go to UniProtKB:  P10827
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T3
Query on T3

Download SDF File 
Download CCD File 
A
3,5,3'TRIIODOTHYRONINE
T3; THYROID HORMONE; LIOTHYRONINE
C15 H12 I3 N O4
AUYYCJSJGJYCDS-LBPRGKRZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 117.569α = 90.00
b = 80.626β = 121.09
c = 62.614γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
MAR345data collection
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2006-07-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description, Structure summary