1YOK

crystal structure of human LRH-1 bound with TIF-2 peptide and phosphatidylglycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.cell.2005.01.024
  • Primary Citation of Related Structures:  1YMT, 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 b ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orphan nuclear receptor NR5A2
A
256Homo sapiensGene Names: NR5A2 (B1F, CPF, FTF)
Find proteins for O00482 (Homo sapiens)
Go to Gene View: NR5A2
Go to UniProtKB:  O00482
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
B, C
14Homo sapiensGene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6L
Query on P6L

Download SDF File 
Download CCD File 
A
(2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE
C40 H75 O10 P
WLVNRDXLPAAELE-GDRYEXQRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.938α = 90.00
b = 67.199β = 90.00
c = 79.569γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2005-07-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance