4LOG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.287 

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
  • Primary Citation of Related Structures:  
    4LOG

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose ABC transporter periplasmic protein and NR2E3 protein chimeric constructAB574Escherichia coli O104:H4 str. 2009EL-2071Homo sapiens
This entity is chimeric
Mutation(s): 1 
Gene Names: ECDH10B_4223malEO3O_01660NR2E3
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q9Y5X4 (Homo sapiens)
Explore Q9Y5X4 
Go to UniProtKB:  Q9Y5X4
NIH Common Fund Data Resources
PHAROS  Q9Y5X4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.285 
  • R-Value Observed: 0.287 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.435α = 90
b = 184.936β = 90
c = 85.97γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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