4IS8 | pdb_00004is8

Divergent sequence tunes ligand sensitivity in phospholipid-regulated hormone receptors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.257 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4IS8

This is version 1.3 of the entry. See complete history

Literature

Divergent Sequence Tunes Ligand Sensitivity in Phospholipid-regulated Hormone Receptors.

Musille, P.M.Pathak, M.Lauer, J.L.Griffin, P.R.Ortlund, E.A.

(2013) J Biological Chem 288: 20702-20712

  • DOI: https://doi.org/10.1074/jbc.M113.472837
  • Primary Citation Related Structures: 
    4IS8

  • PubMed Abstract: 

    The members of the NR5A subfamily of nuclear receptors (NRs) are important regulators of pluripotency, lipid and glucose homeostasis, and steroidogenesis. Liver receptor homologue 1 (LRH-1; NR5A2) and steroidogenic factor 1 (SF-1; NR5A1) have therapeutic potential for the treatment of metabolic and neoplastic disease; however, a poor understanding of their ligand regulation has hampered the pursuit of these proteins as pharmaceutical targets. In this study, we dissect how sequence variation among LRH-1 orthologs affects phospholipid (PL) binding and regulation. Both human LRH-1 (hLRH-1) and mouse LRH-1 (mLRH-1) respond to newly discovered medium chain PL agonists to modulate lipid and glucose homeostasis. These PLs activate hLRH-1 by altering receptor dynamics in a newly identified alternate activation function region. Mouse and Drosophila orthologs contain divergent sequences in this region potentially altering PL-driven activation. Structural evidence suggests that these sequence differences in mLRH-1 and Drosophila FTZ-f1 (dmFTZ-f1) confer at least partial ligand independence, making them poor models for hLRH-1 studies; however, the mechanisms of ligand independence remain untested. We show using structural and biochemical methods that the recent evolutionary divergence of the mLRH-1 stabilizes the active conformation in the absence of ligand, yet does not abrogate PL-dependent activation. We also show by mass spectrometry and biochemical assays that FTZ-f1 is incapable of PL binding. This work provides a structural mechanism for the differential tuning of PL sensitivity in NR5A orthologs and supports the use of mice as viable therapeutic models for LRH-1-dependent diseases.


  • Organizational Affiliation
    • Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA.

Macromolecule Content 

  • Total Structure Weight: 55.69 kDa 
  • Atom Count: 3,752 
  • Modeled Residue Count: 460 
  • Deposited Residue Count: 478 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 5 group A member 2
A, B
239Homo sapiensMutation(s): 6 
Gene Names: B1FCPFFTFNR5A2
UniProt & NIH Common Fund Data Resources
Find proteins for O00482 (Homo sapiens)
Explore O00482 
Go to UniProtKB:  O00482
PHAROS:  O00482
GTEx:  ENSG00000116833 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00482
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.257 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.305α = 90
b = 120.029β = 90
c = 123.838γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2013-07-31
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references