1YMT

Mouse SF-1 LBD

• PDB DOI:  https://doi.org/10.2210/pdb1YMT/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-01-21 Released: 2005-03-15 
• Deposition Author(s): Krylova, I.N., Sablin, E.P., Moore, J., Xu, R.X., Waitt, G.M., Juzumiene, D., Bynum, J.M., Fletterick, R.J., Willson, T.M., Ingraham, H.A.

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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 

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: 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.33 kDa 
• Atom Count: 2,751 
• Modelled Residue Count: 245 
• Deposited Residue Count: 260 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroidogenic factor 1	A	246	Mus musculus	Mutation(s): 4  Gene Names: Nr5a1, Ftzf1
UniProt
Find proteins for P33242 (Mus musculus) Explore P33242  Go to UniProtKB:  P33242

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor 0B2	B	14	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q62227 (Mus musculus) Explore Q62227  Go to UniProtKB:  Q62227
IMPC:  MGI:1346344

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DR9	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 = 73.853	α = 90
b = 73.853	β = 90
c = 117.014	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Krylova, I.N., Sablin, E.P., Moore, J., Xu, R.X., Waitt, G.M., Juzumiene, D., Bynum, J.M., Fletterick, R.J., Willson, T.M., Ingraham, H.A.

Revision History  

• 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