1A6Y

REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.192 

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This is version 1.3 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

  • DOI: https://doi.org/10.1016/s1097-2765(00)80084-2
  • Primary Citation of Related Structures:  
    1A6Y

  • 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 (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

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ORPHAN NUCLEAR RECEPTOR NR1D1C [auth A],
D [auth B]
94Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P20393 (Homo sapiens)
Explore P20393 
Go to UniProtKB:  P20393
PHAROS:  P20393
GTEx:  ENSG00000126368 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20393
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
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')A [auth C]20N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*G)-3')B [auth D]20N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.67α = 75.16
b = 45.69β = 80.64
c = 47.95γ = 85.58
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Data collection, Database references, Derived calculations, Refinement description