1YMT

Mouse SF-1 LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1

Krylova, I.N.Sablin, E.P.Moore, J.Xu, R.X.Waitt, G.M.MacKay, J.A.Juzumiene, D.Bynum, J.M.Madauss, K.Montana, V.Lebedeva, L.Suzawa, M.Williams, J.D.Williams, S.P.Guy, R.K.Thornton, J.W.Fletterick, R.J.Willson, T.M.Ingraham, H.A.

(2005) Cell 120: 343-355

  • DOI: https://doi.org/10.1016/j.cell.2005.01.024
  • Primary Citation of Related Structures:  
    1YMT, 1YOK, 1YOW

  • PubMed Abstract: 

    Vertebrate members of the nuclear receptor NR5A subfamily, which includes steroidogenic factor 1 (SF-1) and liver receptor homolog 1 (LRH-1), regulate crucial aspects of development, endocrine homeostasis, and metabolism. Mouse LRH-1 is believed to be a ligand-independent transcription factor with a large and empty hydrophobic pocket. Here we present structural and biochemical data for three other NR5A members-mouse and human SF-1 and human LRH-1-which reveal that these receptors bind phosphatidyl inositol second messengers and that ligand binding is required for maximal activity. Evolutionary analysis of structure-function relationships across the SF-1/LRH-1 subfamily indicates that ligand binding is the ancestral state of NR5A receptors and was uniquely diminished or altered in the rodent LRH-1 lineage. We propose that phospholipids regulate gene expression by directly binding to NR5A nuclear receptors.


  • Organizational Affiliation

    Department of Physiology, University of California, San Francisco, California 94143, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroidogenic factor 1246Mus musculusMutation(s): 4 
Gene Names: Nr5a1Ftzf1
UniProt
Find proteins for P33242 (Mus musculus)
Explore P33242 
Go to UniProtKB:  P33242
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33242
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor 0B214N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q62227 (Mus musculus)
Explore Q62227 
Go to UniProtKB:  Q62227
IMPC:  MGI:1346344
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62227
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DR9
Query on DR9

Download Ideal Coordinates CCD File 
C [auth A]1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL
C40 H75 O10 P
QGIXWNRQEFVVRM-CTDKCSBDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.853α = 90
b = 73.853β = 90
c = 117.014γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description