7QDT

Crystal structure of a mutant (P393GX) Thyroid Receptor Alpha ligand binding domain designed to model dominant negative human mutations.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted T3Click on this verticalbar to view details

This is version 2.1 of the entry. See complete history


Literature

Structure-Guided Approach to Relieving Transcriptional Repression in Resistance to Thyroid Hormone alpha.

Romartinez-Alonso, B.Agostini, M.Jones, H.McLellan, J.Sood, D.E.Tomkinson, N.Marelli, F.Gentile, I.Visser, W.E.Schoenmakers, E.Fairall, L.Privalsky, M.Moran, C.Persani, L.Chatterjee, K.Schwabe, J.W.R.

(2022) Mol Cell Biol 42: e0036321-e0036321

  • DOI: https://doi.org/10.1128/MCB.00363-21
  • Primary Citation of Related Structures:  
    7QDT

  • PubMed Abstract: 

    Mutations in thyroid hormone receptor α (TRα), a ligand-inducible transcription factor, cause resistance to thyroid hormone α (RTHα). This disorder is characterized by tissue-specific hormone refractoriness and hypothyroidism due to the inhibition of target gene expression by mutant TRα-corepressor complexes. Using biophysical approaches, we show that RTHα-associated TRα mutants devoid of ligand-dependent transcription activation function unexpectedly retain the ability to bind thyroid hormone. Visualization of the ligand T3 within the crystal structure of a prototypic TRα mutant validates this notion. This finding prompted the synthesis of different thyroid hormone analogues, identifying a lead compound, ES08, which dissociates corepressor from mutant human TRα more efficaciously than T3. ES08 rescues developmental anomalies in a zebrafish model of RTHα and induces target gene expression in TRα mutation-containing cells from an RTHα patient more effectively than T3. Our observations provide proof of principle for developing synthetic ligands that can relieve transcriptional repression by the mutant TRα-corepressor complex for treatment of RTHα.


  • Organizational Affiliation

    Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicestergrid.9918.9, Leicester, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform Alpha-1 of Thyroid hormone receptor alpha236Homo sapiensMutation(s): 0 
Gene Names: THRAEAR7ERBA1NR1A1THRA1THRA2
UniProt & NIH Common Fund Data Resources
Find proteins for P10827 (Homo sapiens)
Explore P10827 
Go to UniProtKB:  P10827
PHAROS:  P10827
GTEx:  ENSG00000126351 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10827
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T3 (Subject of Investigation/LOI)
Query on T3

Download Ideal Coordinates CCD File 
B [auth A]3,5,3'TRIIODOTHYRONINE
C15 H12 I3 N O4
AUYYCJSJGJYCDS-LBPRGKRZSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
T3 BindingDB:  7QDT Ki: min: 0.22, max: 2.33 (nM) from 4 assay(s)
Kd: min: 0.06, max: 0.17 (nM) from 4 assay(s)
IC50: min: 0.24, max: 3.2 (nM) from 2 assay(s)
EC50: min: 0.41, max: 30 (nM) from 10 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.328α = 90
b = 143.328β = 90
c = 88.502γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted T3Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Communitys Seventh Framework ProgrammeEuropean UnionPITN-GA-2013-606806

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection
  • Version 2.1: 2024-01-31
    Changes: Refinement description