2V7C

Crystal Structure of Rev-Erb beta

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

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This is version 1.2 of the entry. See complete history. 


Literature

Structural Insight Into the Constitutive Repression Function of the Nuclear Receptor Rev-Erbbeta

Woo, E.-J., Jeong, D.G., Lim, M.-Y., Kim, S.J., Kim, K.-J., Yoon, S.-M., Park, B.-C., Ryu, S.E.

(2007) J Mol Biol 373: 735

  • DOI: 10.1016/j.jmb.2007.08.037
  • Primary Citation of Related Structures:  
    2V0V, 2V7C

  • PubMed Abstract: 

    • The Rev-erb family is an orphan nuclear receptor acting as a negative regulator of transcription. Rev-erbalpha and Rev-erbbeta are crucial components of the circadian clock and involved in various lipid homeostasis. They are unique nuclear receptors that ...

    The Rev-erb family is an orphan nuclear receptor acting as a negative regulator of transcription. Rev-erbalpha and Rev-erbbeta are crucial components of the circadian clock and involved in various lipid homeostasis. They are unique nuclear receptors that lack the activation function 2 helix (AF2-helix) required for ligand-dependent activation by other members of nuclear receptors. Here, we report the crystal structure of Rev-erbbeta (NR1D2) in a dimeric arrangement. The putative ligand-binding pocket (LBP) of Rev-erbbeta is filled with bulky hydrophobic residues resulting in a residual cavity size that is too small to allow binding of any known ligand molecules. However, an alternative conformation of the putative LBP observed in another crystal form suggests the flexibility of this region. The kinked conformation of helix H11 allows helix H11 to bend toward helix H3 over the putative ligand binding pocket by filling and closing the cavity with its side-chains. In the absence of the AF2-helix and a cognate ligand, Rev-erbbeta appears to stabilize the hydrophobic cluster in the putative ligand binding pocket and provide a structural platform for co-repressor binding by adopting the unique geometry of helix H11, a suitable conformation for the constitutive repression activity.

    Organizational Affiliation: 

    Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 52 Eoeun-dong, Yuseonggu, Daejeon, Korea. ejwoo@kribb.re.kr



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORPHAN NUCLEAR RECEPTOR NR1D2 A, B194Homo sapiensMutation(s): 0 
Gene Names: NR1D2
Find proteins for Q14995 (Homo sapiens)
Explore Q14995 
Go to UniProtKB:  Q14995
NIH Common Fund Data Resources
PHAROS:  Q14995
GTEx:  ENSG00000174738
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.677α = 90
b = 71.677β = 90
c = 145.566γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance