Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A1B1C1 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.97 kDa 
• Atom Count: 2253 
• Residue Count: 261 
• Unique protein chains: 2

1YOK

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

• DOI: 10.2210/pdb1YOK/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-01-27 Released: 2005-07-19 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.290 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

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

• PubMed: 15707893 
• DOI: 10.1016/j.cell.2005.01.024
• Primary Citation of Related Structures:  
  1YMT, 1YOW, 1YOK


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orphan nuclear receptor NR5A2	A	256	Homo sapiens	Mutation(s): 0  Gene Names: NR5A2, B1F, CPF, FTF
Find proteins for O00482 (Homo sapiens) Explore O00482  Go to UniProtKB:  O00482
NIH Common Fund Data Resources
PHAROS  O00482 GTEx  ENSG00000116833

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	B, C	14	N/A	Mutation(s): 0
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS  Q15596 GTEx  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6L	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.290 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.938	α = 90
b = 67.199	β = 90
c = 79.569	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-27 
• Released Date: 2005-07-19 
Deposition Author(s): 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.

Revision History 

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