Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 31399.88 
• Atom Count: 2175 
• Residue Count: 267 
• 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


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.007 Å
• R-Value Free: 0.199 
• R-Value Work: 0.171 

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.USA 106: 20717-20722

• PubMed: 19926848 
• DOI: 10.1073/pnas.0911024106
• Primary Citation of Related Structures:  
  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.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
THRA protein	A	267	Homo sapiens	Mutation(s): 0  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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
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: 0.1 nM (100) BINDINGDB
4HY	IC50: ~0.1 nM BINDINGMOAD
4HY	IC50: 0.97 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.007 Å
• R-Value Free: 0.199 
• R-Value Work: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 60.020	α = 90.00
b = 80.825	β = 90.00
c = 102.355	γ = 90.00

Software Package:

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

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
  Type: Version format compliance