5UNJ

Structure of Human Liver Receptor Homolog 1 in complex with PGC1a and RJW100

  • Classification: NUCLEAR PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2017-01-31 Released: 2017-04-19 
  • Deposition Author(s): Mays, S.G., Ortlund, E.A.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.959 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Dynamics of the Liver Receptor Homolog 1-PGC1 alpha Complex.

Mays, S.G.Okafor, C.D.Tuntland, M.L.Whitby, R.J.Dharmarajan, V.Stec, J.Griffin, P.R.Ortlund, E.A.

(2017) Mol. Pharmacol. 92: 1-11

  • DOI: 10.1124/mol.117.108514

  • PubMed Abstract: 
  • Peroxisome proliferator-activated gamma coactivator 1-α (PGC1α) regulates energy metabolism by directly interacting with transcription factors to modulate gene expression. Among the PGC1α binding partners is liver receptor homolog 1 (LRH-1; NR5A2), a ...

    Peroxisome proliferator-activated gamma coactivator 1-α (PGC1α) regulates energy metabolism by directly interacting with transcription factors to modulate gene expression. Among the PGC1α binding partners is liver receptor homolog 1 (LRH-1; NR5A2), an orphan nuclear hormone receptor that controls lipid and glucose homeostasis. Although PGC1α is known to bind and activate LRH-1, mechanisms through which PGC1α changes LRH-1 conformation to drive transcription are unknown. Here, we used biochemical and structural methods to interrogate the LRH-1-PGC1α complex. Purified, full-length LRH-1, as well as isolated ligand binding domain, bound to PGC1α with higher affinity than to the coactivator, nuclear receptor coactivator-2 (Tif2), in coregulator peptide recruitment assays. We present the first crystal structure of the LRH-1-PGC1α complex, which depicts several hydrophobic contacts and a strong charge clamp at the interface between these partners. In molecular dynamics simulations, PGC1α induced correlated atomic motion throughout the entire LRH-1 activation function surface, which was dependent on charge-clamp formation. In contrast, Tif2 induced weaker signaling at the activation function surface than PGC1α but promoted allosteric signaling from the helix 6/β-sheet region of LRH-1 to the activation function surface. These studies are the first to probe mechanisms underlying the LRH-1-PGC1α interaction and may illuminate strategies for selective therapeutic targeting of PGC1α-dependent LRH-1 signaling pathways.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia (S.G.M., C.D.O., M.L.T., E.A.O.); School of Chemistry, University of Southampton, Southampton, United Kingdom (R.J.W., J.S.); and Department of Molecular Medicine, Scripps Research Institute, Jupiter, Florida (V.D., P.R.G.).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 5 group A member 2
A
245Homo sapiensMutation(s): 0 
Gene Names: NR5A2 (B1F, CPF, FTF)
Find proteins for O00482 (Homo sapiens)
Go to Gene View: NR5A2
Go to UniProtKB:  O00482
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated gamma coactivator 1-alpha
C
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RJW
Query on RJW

Download SDF File 
Download CCD File 
A
(1R,3aR,6aR)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-ol
C28 H34 O
ZFXMYHPLTQTTFW-REUBFRLUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RJWKd: 240 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.959 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.180α = 90.00
b = 84.027β = 90.00
c = 45.355γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesR01DK095750
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesF31DK111171
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32GM008602
National Institutes of Health/National Institute of General Medical SciencesUnited StatesNIH K12GM000680

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Refinement description