3CQV

Crystal structure of Reverb beta in complex with heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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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
  • Primary Citation of Related Structures:  
    3CQV

  • 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, inflammation, and cancer ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor subfamily 1 group D member 2A199Homo sapiensMutation(s): 0 
Gene Names: NR1D2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14995 (Homo sapiens)
Explore Q14995 
Go to UniProtKB:  Q14995
PHAROS:  Q14995
GTEx:  ENSG00000174738 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14995
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
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: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.428α = 90
b = 48.623β = 90
c = 68.954γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

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