4LNX

Crystal structure of TR-alpha bound to T4 in a second site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of a new hormone-binding site on the surface of thyroid hormone receptor.

Souza, P.C.Puhl, A.C.Martinez, L.Aparicio, R.Nascimento, A.S.Figueira, A.C.Nguyen, P.Webb, P.Skaf, M.S.Polikarpov, I.

(2014) Mol.Endocrinol. 28: 534-545

  • DOI: 10.1210/me.2013-1359
  • Primary Citation of Related Structures:  4LNW

  • PubMed Abstract: 
  • Thyroid hormone receptors (TRs) are members of the nuclear receptor superfamily of ligand-activated transcription factors involved in cell differentiation, growth, and homeostasis. Although X-ray structures of many nuclear receptor ligand-binding dom ...

    Thyroid hormone receptors (TRs) are members of the nuclear receptor superfamily of ligand-activated transcription factors involved in cell differentiation, growth, and homeostasis. Although X-ray structures of many nuclear receptor ligand-binding domains (LBDs) reveal that the ligand binds within the hydrophobic core of the ligand-binding pocket, a few studies suggest the possibility of ligands binding to other sites. Here, we report a new x-ray crystallographic structure of TR-LBD that shows a second binding site for T3 and T4 located between H9, H10, and H11 of the TRα LBD surface. Statistical multiple sequence analysis, site-directed mutagenesis, and cell transactivation assays indicate that residues of the second binding site could be important for the TR function. We also conducted molecular dynamics simulations to investigate ligand mobility and ligand-protein interaction for T3 and T4 bound to this new TR surface-binding site. Extensive molecular dynamics simulations designed to compute ligand-protein dissociation constant indicate that the binding affinities to this surface site are of the order of the plasma and intracellular concentrations of the thyroid hormones, suggesting that ligands may bind to this new binding site under physiological conditions. Therefore, the second binding site could be useful as a new target site for drug design and could modulate selectively TR functions.


    Organizational Affiliation

    Institute of Chemistry (P.C.T.S., L.M., R.A., M.S.S.), State University of Campinas-UNICAMP, Campinas, Sao Paulo, Brazil; Institute of Physics of São Carlos (A.C.P., A.S.N., P.W., I.P.), University of São Paulo-USP, São Carlos, Sao Paulo, Brazil; National Laboratory of Biosciences (A.C.M.F.), CNPEM, Campinas, Sao Paulo, Brazil; University of California Medical Center (P.N.), Diabetes Center, San Francisco, California; and Genomic Medicine (P.W.), Houston Methodist Research Institute, Houston, Texas.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thyroid hormone receptor alpha
A
267Homo sapiensGene 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 2 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
T44
Query on T44

Download SDF File 
Download CCD File 
A
3,5,3',5'-TETRAIODO-L-THYRONINE
C15 H11 I4 N O4
XUIIKFGFIJCVMT-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: 2.05 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.744α = 90.00
b = 80.924β = 90.00
c = 101.871γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
PHENIXrefinement
MAR345dtbdata collection
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Database references