5SYZ

Human Liver Receptor Homologue-1 (LRH-1) Bound to a RJW100 stereoisomer and a Fragment of TIF-2

  • Classification: NUCLEAR PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Enterobacteria phage L1

  • Deposited: 2016-08-12 Released: 2016-10-12 
  • Deposition Author(s): Ortlund, E.A., Mays, S.G.
  • 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: 1.9261 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of the Nuclear Receptor, Liver Receptor Homolog 1, Bound to Synthetic Agonists.

Mays, S.G.Okafor, C.D.Whitby, R.J.Goswami, D.Stec, J.Flynn, A.R.Dugan, M.C.Jui, N.T.Griffin, P.R.Ortlund, E.A.

(2016) J. Biol. Chem. 291: 25281-25291

  • DOI: 10.1074/jbc.M116.753541
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Liver receptor homolog 1 (NR5A2, LRH-1) is an orphan nuclear hormone receptor that regulates diverse biological processes, including metabolism, proliferation, and the resolution of endoplasmic reticulum stress. Although preclinical and cellular stud ...

    Liver receptor homolog 1 (NR5A2, LRH-1) is an orphan nuclear hormone receptor that regulates diverse biological processes, including metabolism, proliferation, and the resolution of endoplasmic reticulum stress. Although preclinical and cellular studies demonstrate that LRH-1 has great potential as a therapeutic target for metabolic diseases and cancer, development of LRH-1 modulators has been difficult. Recently, systematic modifications to one of the few known chemical scaffolds capable of activating LRH-1 failed to improve efficacy substantially. Moreover, mechanisms through which LRH-1 is activated by synthetic ligands are entirely unknown. Here, we use x-ray crystallography and other structural methods to explore conformational changes and receptor-ligand interactions associated with LRH-1 activation by a set of related agonists. Unlike phospholipid LRH-1 ligands, these agonists bind deep in the pocket and do not interact with residues near the mouth nor do they expand the pocket like phospholipids. Unexpectedly, two closely related agonists with similar efficacies (GSK8470 and RJW100) exhibit completely different binding modes. The dramatic repositioning is influenced by a differential ability to establish stable face-to-face π-π-stacking with the LRH-1 residue His-390, as well as by a novel polar interaction mediated by the RJW100 hydroxyl group. The differing binding modes result in distinct mechanisms of action for the two agonists. Finally, we identify a network of conserved water molecules near the ligand-binding site that are important for activation by both agonists. This work reveals a previously unappreciated complexity associated with LRH-1 agonist development and offers insights into rational design strategies.


    Organizational Affiliation

    From the Department of Biochemistry, Emory University School of Medicine, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 5 group A member 2
A
242Homo 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
Nuclear receptor coactivator 2
C
15Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
71W
Query on 71W

Download SDF File 
Download CCD File 
A
(1S,3aR,6aR)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-ol
C28 H34 O
ZFXMYHPLTQTTFW-NSVAZKTRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
71WEC50: 398.1 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9261 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 46.312α = 90.00
b = 46.312β = 90.00
c = 219.966γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data scaling

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

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references
  • Version 1.2: 2016-12-14
    Type: Database references
  • Version 1.3: 2017-09-06
    Type: Author supporting evidence