Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.40 kDa 
• Atom Count: 2421 
• Residue Count: 264 
• Unique protein chains: 1

3JZB

Crystal Structure of TR-alfa bound to the selective thyromimetic TRIAC

• DOI: 10.2210/pdb3JZB/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-23 Released: 2009-12-08 
• Deposition Author(s): Nascimento, A.S., Dias, S.M.G., Nunes, F.M., Aparicio, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.199 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Literature

Gaining ligand selectivity in thyroid hormone receptors via entropy.

Martinez, L., Nascimento, A.S., Nunes, F.M., Phillips, K., Aparicio, R., Dias, S.M., Figueira, A.C., Lin, J.H., Nguyen, P., Apriletti, J.W., Neves, F.A., Baxter, J.D., Webb, P., Skaf, M.S., Polikarpov, I.

(2009) Proc Natl Acad Sci U S A 106: 20717-20722

• PubMed: 19926848 
• DOI: 10.1073/pnas.0911024106
• Primary Citation of Related Structures:  
  3JZB, 3JZC


• PubMed Abstract: 
  

Nuclear receptors are important targets for pharmaceuticals, but similarities between family members cause difficulties in obtaining highly selective compounds. Synthetic ligands that are selective for thyroid hormone (TH) receptor beta (TRbeta) vs. TRalpha reduce cholesterol and fat without effects on heart rate; thus, it is important to understand TRbeta-selective binding. Binding of 3 selective ligands (GC-1, KB141, and GC-24) is characterized at the atomic level; preferential binding depends on a nonconserved residue (Asn-331beta) in the TRbeta ligand-binding cavity (LBC), and GC-24 gains extra selectivity from insertion of a bulky side group into an extension of the LBC that only opens up with this ligand. Here we report that the natural TH 3,5,3'-triodothyroacetic acid (Triac) exhibits a previously unrecognized mechanism of TRbeta selectivity. TR x-ray structures reveal better fit of ligand with the TRalpha LBC. The TRbeta LBC, however, expands relative to TRalpha in the presence of Triac (549 A(3) vs. 461 A(3)), and molecular dynamics simulations reveal that water occupies the extra space. Increased solvation compensates for weaker interactions of ligand with TRbeta and permits greater flexibility of the Triac carboxylate group in TRbeta than in TRalpha. We propose that this effect results in lower entropic restraint and decreases free energy of interactions between Triac and TRbeta, explaining subtype-selective binding. Similar effects could potentially be exploited in nuclear receptor drug design.

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Organizational Affiliation: 

Instituto de Química, Universidade Estadual de Campinas, SP 13084-862, Campinas, Brazil.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THRA protein	A	267	Homo sapiens	Mutation(s): 0  Gene Names: THRA, hCG_1749555, EAR7, ERBA1, NR1A1, THRA1, THRA2
Find proteins for P10827 (Homo sapiens) Explore P10827  Go to UniProtKB:  P10827
NIH Common Fund Data Resources
PHAROS  P10827 GTEx  ENSG00000126351

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4HY	A	[4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID C14 H9 I3 O4 UOWZUVNAGUAEQC-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS	A	L-PEPTIDE LINKING	C5 H12 As N O2 S		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4HY	IC50:  0.10000000149011612   nM  Binding MOAD
4HY	IC50 :  0.9700000286102295   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.199 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.02	α = 90
b = 80.825	β = 90
c = 102.355	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-23 
• Released Date: 2009-12-08 
Deposition Author(s): Nascimento, A.S., Dias, S.M.G., Nunes, F.M., Aparicio, R.

Revision History 

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance