4QJR

Crystal structure of human nuclear receptor sf-1 (nr5a1) bound to its hormone pip3 at 2.4 a resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The signaling phospholipid PIP3 creates a new interaction surface on the nuclear receptor SF-1.

Blind, R.D.Sablin, E.P.Kuchenbecker, K.M.Chiu, H.J.Deacon, A.M.Das, D.Fletterick, R.J.Ingraham, H.A.

(2014) Proc.Natl.Acad.Sci.USA 111: 15054-15059

  • DOI: 10.1073/pnas.1416740111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The signaling phosphatidylinositol lipids PI(4,5)P2 (PIP2) and PI(3,4,5)P3 (PIP3) bind nuclear receptor 5A family (NR5As), but their regulatory mechanisms remain unknown. Here, the crystal structures of human NR5A1 (steroidogenic factor-1, SF-1) liga ...

    The signaling phosphatidylinositol lipids PI(4,5)P2 (PIP2) and PI(3,4,5)P3 (PIP3) bind nuclear receptor 5A family (NR5As), but their regulatory mechanisms remain unknown. Here, the crystal structures of human NR5A1 (steroidogenic factor-1, SF-1) ligand binding domain (LBD) bound to PIP2 and PIP3 show the lipid hydrophobic tails sequestered in the hormone pocket, as predicted. However, unlike classic nuclear receptor hormones, the phosphoinositide head groups are fully solvent-exposed and complete the LBD fold by organizing the receptor architecture at the hormone pocket entrance. The highest affinity phosphoinositide ligand PIP3 stabilizes the coactivator binding groove and increases coactivator peptide recruitment. This receptor-ligand topology defines a previously unidentified regulatory protein-lipid surface on SF-1 with the phosphoinositide head group at its nexus and poised to interact with other proteins. This surface on SF-1 coincides with the predicted binding site of the corepressor DAX-1 (dosage-sensitive sex reversal, adrenal hypoplasia critical region on chromosome X), and importantly harbors missense mutations associated with human endocrine disorders. Our data provide the structural basis for this poorly understood cluster of human SF-1 mutations and demonstrates how signaling phosphoinositides function as regulatory ligands for NR5As.


    Organizational Affiliation

    Departments of Cellular and Molecular Pharmacology and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Steroidogenic factor 1
A
245Homo sapiensMutation(s): 2 
Gene Names: NR5A1 (AD4BP, FTZF1, SF1)
Find proteins for Q13285 (Homo sapiens)
Go to Gene View: NR5A1
Go to UniProtKB:  Q13285
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
B
14Homo sapiensMutation(s): 0 
Gene Names: PPARGC1A (LEM6, PGC1, PGC1A, PPARGC1)
Find proteins for Q9UBK2 (Homo sapiens)
Go to Gene View: PPARGC1A
Go to UniProtKB:  Q9UBK2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PIZ
Query on PIZ

Download SDF File 
Download CCD File 
A
(2S)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane-1,2-diyl dihexadecanoate
PI(3,4,5)P3 dipalmitoyl (16:0, 16:0)
C41 H82 O22 P4
ZSZXYWFCIKKZBT-XMZWCAJNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PIZKd: 80 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 74.850α = 90.00
b = 74.850β = 90.00
c = 139.630γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MolProbitymodel building
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-11-12
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description