2RIW | pdb_00002riw

The Reactive loop cleaved human Thyroxine Binding Globulin complexed with thyroxine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.244 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2RIW

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Allosteric modulation of hormone release from thyroxine and corticosteroid-binding globulins

Qi, X.Loiseau, F.Chan, W.L.Yan, Y.Wei, Z.Milroy, L.G.Myers, R.M.Ley, S.V.Read, R.J.Carrell, R.W.Zhou, A.

(2011) J Biological Chem 286: 16163-16173

  • DOI: https://doi.org/10.1074/jbc.M110.171082
  • Primary Citation Related Structures: 
    2RIV, 2RIW, 2XN3, 2XN5, 2XN6, 2XN7

  • PubMed Abstract: 

    The release of hormones from thyroxine-binding globulin (TBG) and corticosteroid-binding globulin (CBG) is regulated by movement of the reactive center loop in and out of the β-sheet A of the molecule. To investigate how these changes are transmitted to the hormone-binding site, we developed a sensitive assay using a synthesized thyroxine fluorophore and solved the crystal structures of reactive loop cleaved TBG together with its complexes with thyroxine, the thyroxine fluorophores, furosemide, and mefenamic acid. Cleavage of the reactive loop results in its complete insertion into the β-sheet A and a substantial but incomplete decrease in binding affinity in both TBG and CBG. We show here that the direct interaction between residue Thr(342) of the reactive loop and Tyr(241) of the hormone binding site contributes to thyroxine binding and release following reactive loop insertion. However, a much larger effect occurs allosterically due to stretching of the connecting loop to the top of the D helix (hD), as confirmed in TBG with shortening of the loop by three residues, making it insensitive to the S-to-R transition. The transmission of the changes in the hD loop to the binding pocket is seen to involve coherent movements in the s2/3B loop linked to the hD loop by Lys(243), which is, in turn, linked to the s4/5B loop, flanking the thyroxine-binding site, by Arg(378). Overall, the coordinated movements of the reactive loop, hD, and the hormone binding site allow the allosteric regulation of hormone release, as with the modulation demonstrated here in response to changes in temperature.


  • Organizational Affiliation
    • Department of Biochemistry, Nanjing University, Nanjing, China.

Macromolecule Content 

  • Total Structure Weight: 43.27 kDa 
  • Atom Count: 3,282 
  • Modeled Residue Count: 371 
  • Deposited Residue Count: 378 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thyroxine-binding globulin338Homo sapiensMutation(s): 0 
Gene Names: SERPINA7TBG
UniProt & NIH Common Fund Data Resources
Find proteins for P05543 (Homo sapiens)
Explore P05543 
Go to UniProtKB:  P05543
PHAROS:  P05543
GTEx:  ENSG00000123561 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05543
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Thyroxine-binding globulin40Homo sapiensMutation(s): 0 
Gene Names: SERPINA7TBG
UniProt & NIH Common Fund Data Resources
Find proteins for P05543 (Homo sapiens)
Explore P05543 
Go to UniProtKB:  P05543
PHAROS:  P05543
GTEx:  ENSG00000123561 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05543
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T44

Query on T44



Download:Ideal Coordinates CCD File
C [auth A]3,5,3',5'-TETRAIODO-L-THYRONINE
C15 H11 I4 N O4
XUIIKFGFIJCVMT-LBPRGKRZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.244 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.594α = 90
b = 42.164β = 90
c = 55.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-01-16
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection