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 
  • R-Value Observed: 0.157 

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, 4LNX

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thyroid hormone receptor alpha A267Homo sapiensMutation(s): 0 
Gene Names: THRAEAR7ERBA1NR1A1THRA1THRA2
Find proteins for P10827 (Homo sapiens)
Explore P10827 
Go to UniProtKB:  P10827
NIH Common Fund Data Resources
PHAROS:  P10827
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T44
Query on T44

Download Ideal Coordinates CCD File 
A
3,5,3',5'-TETRAIODO-L-THYRONINE
C15 H11 I4 N O4
XUIIKFGFIJCVMT-LBPRGKRZSA-N
 Ligand Interaction
T3
Query on T3

Download Ideal Coordinates CCD File 
A
3,5,3'TRIIODOTHYRONINE
C15 H12 I3 N O4
AUYYCJSJGJYCDS-LBPRGKRZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
AL-PEPTIDE LINKINGC5 H12 As N O2 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T3Ki:  0.33000001311302185   nM  BindingDB
T3Kd:  0.10000000149011612   nM  BindingDB
T3Ki:  2.299999952316284   nM  BindingDB
T3EC50:  2.0999999046325684   nM  BindingDB
T3IC50:  0.23999999463558197   nM  BindingDB
T3Ki:  0.2199999988079071   nM  BindingDB
T3IC50:  3.200000047683716   nM  BindingDB
T3EC50:  2.4000000953674316   nM  BindingDB
T3Kd:  0.05999999865889549   nM  BindingDB
T3Ki:  2.3299999237060547   nM  BindingDB
T3EC50:  2   nM  BindingDB
T3EC50:  1.0099999904632568   nM  BindingDB
T3EC50:  0.4099999964237213   nM  BindingDB
T3Kd:  0.17000000178813934   nM  BindingDB
T3EC50:  10   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.744α = 90
b = 80.924β = 90
c = 101.871γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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