2V0V

Crystal Structure of Rev-Erb beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.220 

wwPDB Validation 3D Report Full Report


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.Jun Kim, S.Kim, K.-J.Yoon, S.-M.Park, B.-C.Eon Ryu, S.

(2007) J.Mol.Biol. 373: 735

  • DOI: 10.1016/j.jmb.2007.08.037
  • Primary Citation of Related Structures:  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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORPHAN NUCLEAR RECEPTOR NR1D2
A, B, C, D
194Homo sapiensGene Names: NR1D2
Find proteins for Q14995 (Homo sapiens)
Go to Gene View: NR1D2
Go to UniProtKB:  Q14995
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.220 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 102.456α = 90.00
b = 102.456β = 90.00
c = 143.964γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
HKL-2000data reduction
HKL-2000data scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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