1ZDT

The Crystal Structure of Human Steroidogenic Factor-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.265 (Depositor) 
  • R-Value Work: 
    0.216 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

The crystal structures of human steroidogenic factor-1 and liver receptor homologue-1

Wang, W.Zhang, C.Marimuthu, A.Krupka, H.I.Tabrizizad, M.Shelloe, R.Mehra, U.Eng, K.Nguyen, H.Settachatgul, C.Powell, B.Milburn, M.V.West, B.L.

(2005) Proc Natl Acad Sci U S A 102: 7505-7510

  • DOI: https://doi.org/10.1073/pnas.0409482102
  • Primary Citation of Related Structures:  
    1ZDT, 1ZDU

  • PubMed Abstract: 

    Steroidogenic factor-1 (SF-1) and liver receptor homologue-1 (LRH-1) belong to the fushi tarazu factor 1 subfamily of nuclear receptors. SF-1 is an essential factor for sex determination during development and regulates adrenal and gonadal steroidogenesis in the adult, whereas LRH-1 is a critical factor for development of endodermal tissues and regulates cholesterol and bile acid homeostasis. Regulatory ligands are unknown for SF-1 and LRH-1. A reported mouse LRH-1 structure revealed an empty pocket in a region commonly occupied by ligands in the structures of other nuclear receptors, and pocket-filling mutations did not alter the constitutive activity observed. Here we report the crystal structures of the putative ligand-binding domains of human SF-1 at 2.1-A resolution and human LRH-1 at 2.5-A resolution. Both structures bind a coactivator-derived peptide at the canonical activation-function surface, thus adopting the transcriptionally activating conformation. In human LRH-1, coactivator peptide binding also occurs to a second site. We discovered in both structures a phospholipid molecule bound in a pocket of the putative ligand-binding domain. MS analysis of the protein samples used for crystallization indicated that the two proteins associate with a range of phospholipids. Mutations of the pocket-lining residues reduced the transcriptional activities of SF-1 and LRH-1 in mammalian cell transfection assays without affecting their expression levels. These results suggest that human SF-1 and LRH-1 may be ligand-binding receptors, although it remains to be seen if phospholipids or possibly other molecules regulate SF-1 or LRH-1 under physiological conditions.


  • Organizational Affiliation

    Plexxikon, Inc., 91 Bolivar Drive, Berkeley, CA 94710, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroidogenic factor 1
A, B
241Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13285 (Homo sapiens)
Explore Q13285 
Go to UniProtKB:  Q13285
PHAROS:  Q13285
GTEx:  ENSG00000136931 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13285
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2C [auth P],
D [auth Q]
12N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.265 (Depositor) 
  • R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.601α = 90
b = 73.601β = 90
c = 195.678γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
EPMRphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PEFClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection