3F7D

SF-1 LBD bound by phosphatidylcholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of SF-1 bound by different phospholipids: evidence for regulatory ligands.

Sablin, E.P.Blind, R.D.Krylova, I.N.Ingraham, J.G.Cai, F.Williams, J.D.Fletterick, R.J.Ingraham, H.A.

(2009) Mol.Endocrinol. 23: 25-34

  • DOI: 10.1210/me.2007-0508

  • PubMed Abstract: 
  • Despite the fact that many nuclear receptors are ligand dependent, the existence of obligate regulatory ligands is debated for some receptors, including steroidogenic factor 1 (SF-1). Although fortuitously bound bacterial phospholipids were discovere ...

    Despite the fact that many nuclear receptors are ligand dependent, the existence of obligate regulatory ligands is debated for some receptors, including steroidogenic factor 1 (SF-1). Although fortuitously bound bacterial phospholipids were discovered in the structures of the SF-1 ligand-binding domain (LBD), these lipids might serve merely as structural ligands. Thus, we examined whether exogenously added phospholipids would exchange for these bacterial lipids and bind to SF-1. Here, we report the first crystal structure of the SF-1 LBD bound by the exchanged phosphatidylcholine. Although the bound phosphatidylcholine phospholipid mimics the conformation of bound bacterial phosphoplipids, two surface loops, L2-3 and L11-12, surrounding the entrance to the pocket vary significantly between different SF-1 LBD structures. Based on this observation, we hypothesized that a bound ligand might control the conformations of loops L2-3 and L11-12, and that conserved residues in these dynamic loops could influence ligand binding and the receptor function. Consistent with this hypothesis, impaired phospholipid exchange and diminished transcriptional activity were observed for loop L11-12 SF-1 mutants and for the loop L2-3 human mutant R255L. The endocrine disease associated with this L2-3 mutation coupled with our cellular and biochemical data suggest that critical residues at the mouth of the ligand-binding pocket have evolved for efficient binding of phospholipid ligands and for achieving optimal SF-1 activity.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
nuclear receptor SF-1
A
244Mus musculusMutation(s): 4 
Gene Names: Nr5a1 (Ftzf1)
Find proteins for P33242 (Mus musculus)
Go to UniProtKB:  P33242
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
B
14Mus musculusMutation(s): 0 
Gene Names: Ppargc1a (Pgc1, Pgc1a, Ppargc1)
Find proteins for O70343 (Mus musculus)
Go to UniProtKB:  O70343
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P42
Query on P42

Download SDF File 
Download CCD File 
A
(2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate
1-Stearoyl-2-Palmitoyl-sn-Glycero-3-Phosphocholine
C42 H88 N O8 P
LYKCEYRWVRQPBD-FEWNNGCESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAF
Query on CAF
A
L-PEPTIDE LINKINGC5 H12 As N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.895α = 90.00
b = 67.228β = 90.00
c = 82.689γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
CNSrefinement
CNSphasing
ADSCdata collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-04-02
    Type: Source and taxonomy
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description