4LOG

The crystal structure of the orphan nuclear receptor PNR ligand binding domain fused with MBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.285 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of the Orphan Nuclear Receptor NR2E3/PNR Ligand Binding Domain Reveals a Dimeric Auto-Repressed Conformation.

Tan, M.H.Zhou, X.E.Soon, F.F.Li, X.Li, J.Yong, E.L.Melcher, K.Xu, H.E.

(2013) Plos One 8: e74359-e74359

  • DOI: 10.1371/journal.pone.0074359

  • PubMed Abstract: 
  • Photoreceptor-specific nuclear receptor (PNR, NR2E3) is a key transcriptional regulator of human photoreceptor differentiation and maintenance. Mutations in the NR2E3-encoding gene cause various retinal degenerations, including Enhanced S-cone syndro ...

    Photoreceptor-specific nuclear receptor (PNR, NR2E3) is a key transcriptional regulator of human photoreceptor differentiation and maintenance. Mutations in the NR2E3-encoding gene cause various retinal degenerations, including Enhanced S-cone syndrome, retinitis pigmentosa, and Goldman-Favre disease. Although physiological ligands have not been identified, it is believed that binding of small molecule agonists, receptor desumoylation, and receptor heterodimerization may switch NR2E3 from a transcriptional repressor to an activator. While these features make NR2E3 a potential therapeutic target for the treatment of retinal diseases, there has been a clear lack of structural information for the receptor. Here, we report the crystal structure of the apo NR2E3 ligand binding domain (LBD) at 2.8 Å resolution. Apo NR2E3 functions as transcriptional repressor in cells and the structure of its LBD is in a dimeric auto-repressed conformation. In this conformation, the putative ligand binding pocket is filled with bulky hydrophobic residues and the activation-function-2 (AF2) helix occupies the canonical cofactor binding site. Mutations designed to disrupt either the AF2/cofactor-binding site interface or the dimer interface compromised the transcriptional repressor activity of this receptor. Together, these results reveal several conserved structural features shared by related orphan nuclear receptors, suggest that most disease-causing mutations affect the receptor's structural integrity, and allowed us to model a putative active conformation that can accommodate small ligands in its pocket.


    Organizational Affiliation

    Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan, United States of America ; Department of Obstetrics & Gynecology, National University Hospital, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose ABC transporter periplasmic protein and NR2E3 protein chimeric construct
A, B
574Homo sapiensEscherichia coli (strain K12)
This entity is chimeric
Mutation(s): 1 
Gene Names: NR2E3 (PNR, RNR), malE
Find proteins for Q9Y5X4 (Homo sapiens)
Go to Gene View: NR2E3
Go to UniProtKB:  Q9Y5X4
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.285 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 89.435α = 90.00
b = 184.936β = 90.00
c = 85.970γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Refinement description, Source and taxonomy
  • Version 1.2: 2017-11-15
    Type: Refinement description