4N73

Crystal structure of the ligand binding domain (LBD) of REV-ERB beta bound to Cobalt Protoporphyrin IX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8662 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of REV-ERB beta Ligand-binding Domain Bound to a Porphyrin Antagonist.

Matta-Camacho, E.Banerjee, S.Hughes, T.S.Solt, L.A.Wang, Y.Burris, T.P.Kojetin, D.J.

(2014) J.Biol.Chem. 289: 20054-20066

  • DOI: 10.1074/jbc.M113.545111

  • PubMed Abstract: 
  • REV-ERBα and REV-ERBβ are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors that play important roles in the regulation of circadian physiology, metabolism, and immune function. Although the REV-ERBs were orig ...

    REV-ERBα and REV-ERBβ are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors that play important roles in the regulation of circadian physiology, metabolism, and immune function. Although the REV-ERBs were originally characterized as orphan receptors, recent studies have demonstrated that they function as receptors for heme. Here, we demonstrate that cobalt protoporphyrin IX (CoPP) and zinc protoporphyrin IX (ZnPP) are ligands that bind directly to the REV-ERBs. However, instead of mimicking the agonist action of heme, CoPP and ZnPP function as antagonists of REV-ERB function. This was unexpected because the only distinction between these ligands is the metal ion that is coordinated. To understand the structural basis by which REV-ERBβ can differentiate between a porphyrin agonist and antagonist, we characterized the interaction between REV-ERBβ with heme, CoPP, and ZnPP using biochemical and structural approaches, including x-ray crystallography and NMR. The crystal structure of CoPP-bound REV-ERBβ indicates only minor conformational changes induced by CoPP compared with heme, including the porphyrin ring of CoPP, which adopts a planar conformation as opposed to the puckered conformation observed in the heme-bound REV-ERBβ crystal structure. Thus, subtle changes in the porphyrin metal center and ring conformation may influence the agonist versus antagonist action of porphyrins and when considered with other studies suggest that gas binding to the iron metal center heme may drive alterations in REV-ERB activity.


    Organizational Affiliation

    From the Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33418 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 1 group D member 2
A
199Homo sapiensMutation(s): 1 
Gene Names: NR1D2
Find proteins for Q14995 (Homo sapiens)
Go to Gene View: NR1D2
Go to UniProtKB:  Q14995
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COH
Query on COH

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING CO
C34 H32 Co N4 O4
AQTFKGDWFRRIHR-CTESUSPADG
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8662 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.660α = 90.00
b = 48.680β = 90.00
c = 69.750γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references
  • Version 1.2: 2014-07-30
    Type: Database references
  • Version 1.3: 2018-03-14
    Type: Database references