3CQV

Crystal structure of Reverb beta in complex with heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta.

Pardee, K.I.Xu, X.Reinking, J.Schuetz, A.Dong, A.Liu, S.Zhang, R.Tiefenbach, J.Lajoie, G.Plotnikov, A.N.Botchkarev, A.Krause, H.M.Edwards, A.

(2009) Plos Biol. 7: e43-e43

  • DOI: 10.1371/journal.pbio.1000043

  • PubMed Abstract: 
  • Heme is a ligand for the human nuclear receptors (NR) REV-ERBalpha and REV-ERBbeta, which are transcriptional repressors that play important roles in circadian rhythm, lipid and glucose metabolism, and diseases such as diabetes, atherosclerosis, infl ...

    Heme is a ligand for the human nuclear receptors (NR) REV-ERBalpha and REV-ERBbeta, which are transcriptional repressors that play important roles in circadian rhythm, lipid and glucose metabolism, and diseases such as diabetes, atherosclerosis, inflammation, and cancer. Here we show that transcription repression mediated by heme-bound REV-ERBs is reversed by the addition of nitric oxide (NO), and that the heme and NO effects are mediated by the C-terminal ligand-binding domain (LBD). A 1.9 A crystal structure of the REV-ERBbeta LBD, in complex with the oxidized Fe(III) form of heme, shows that heme binds in a prototypical NR ligand-binding pocket, where the heme iron is coordinately bound by histidine 568 and cysteine 384. Under reducing conditions, spectroscopic studies of the heme-REV-ERBbeta complex reveal that the Fe(II) form of the LBD transitions between penta-coordinated and hexa-coordinated structural states, neither of which possess the Cys384 bond observed in the oxidized state. In addition, the Fe(II) LBD is also able to bind either NO or CO, revealing a total of at least six structural states of the protein. The binding of known co-repressors is shown to be highly dependent upon these various liganded states. REV-ERBs are thus highly dynamic receptors that are responsive not only to heme, but also to redox and gas. Taken together, these findings suggest new mechanisms for the systemic coordination of molecular clocks and metabolism. They also raise the possibility for gas-based therapies for the many disorders associated with REV-ERB biological functions.


    Organizational Affiliation

    Banting and Best Department of Medical Research, The Department of Molecular Genetics, University of Toronto, Toronto, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 1 group D member 2
A
199Homo sapiensMutation(s): 0 
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
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 73.428α = 90.00
b = 48.623β = 90.00
c = 68.954γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
HKL-3000data reduction
HKL-3000data collection
HKL-3000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance