1A6Y

REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural elements of an orphan nuclear receptor-DNA complex.

Zhao, Q.Khorasanizadeh, S.Miyoshi, Y.Lazar, M.A.Rastinejad, F.

(1998) Mol.Cell 1: 849-861


  • PubMed Abstract: 
  • The nuclear hormone receptors form the largest known family of transcription factors. The current notion of receptor DNA discrimination, based solely on one major type of hexameric half-site and a highly conserved 66-residue core DNA-binding domain ( ...

    The nuclear hormone receptors form the largest known family of transcription factors. The current notion of receptor DNA discrimination, based solely on one major type of hexameric half-site and a highly conserved 66-residue core DNA-binding domain (DBD), does not adequately describe how more than 150 nonsteroid receptors differentiate among response elements. Here, we describe the 2.3 A crystal structure of the DNA-binding region of the orphan receptor RevErb arranged as a tandem homodimer on its optimal response element. The structure reveals the presence of a second major protein-DNA interface adjacent to the classical one involving the half-sites. A sequence comparison of orphan receptors suggests that unique minor-groove interactions involving the receptor hinge regions impart the necessary DNA and dimerization specificity.


    Organizational Affiliation

    Department of Pharmacology, School of Medicine, University of Virginia, Charlottesville 22908, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ORPHAN NUCLEAR RECEPTOR NR1D1
A, B
94Homo sapiensGene Names: NR1D1 (EAR1, HREV, THRAL)
Find proteins for P20393 (Homo sapiens)
Go to Gene View: NR1D1
Go to UniProtKB:  P20393
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*(5IT)P*AP*GP*GP*TP*CP*AP*G)-3')C20N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*G)-3')D20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
C
DNA LINKINGC9 H12 I N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.192 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.670α = 75.16
b = 45.690β = 80.64
c = 47.950γ = 85.58
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance