Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 30708.59 
• Atom Count: 2149 
• Residue Count: 259 
• Unique protein chains: 2

4QK4

Crystal structure of human nuclear receptor sf-1 (nr5a1) bound to pip2 at 2.8 a resolution

• DOI: 10.2210/pdb4QK4/pdb

• Classification: TRANSCRIPTION FACTOR/HORMONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2014-06-05 Released: 2014-07-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.241 
• R-Value Work: 0.200 

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

• PubMed: 25288771 
• DOI: 10.1073/pnas.1416740111
• Primary Citation of Related Structures:  
  4QJR


• 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) 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
Molecule	Chains	Sequence Length	Organism	Details
Steroidogenic factor 1	A	245	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha	B	14	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PIK	A	(2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate PI(4,5)P2 dipalmitoyl (16:0,16:0) C41 H81 O19 P3 HKWJHKSHEWVOSS-MVLQGUJPSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.241 
• R-Value Work: 0.200 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data DOI: 
  10.18430/M34QK4 Protein Diffraction

Unit Cell:

Length (Å)	Angle (°)
a = 75.000	α = 90.00
b = 75.000	β = 90.00
c = 138.630	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
MolProbity	model building
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-05 
• Released Date: 2014-07-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

Revision History 

• Version 1.0: 2014-07-30
  Type: Initial release
• Version 1.1: 2015-02-04
  Type: Database references
• Version 1.2: 2017-11-22
  Type: Refinement description
• Version 1.3: 2018-03-07
  Type: Data collection