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 1.2 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

  • DOI: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
ORPHAN NUCLEAR RECEPTOR NR1D1C [auth A],
D [auth B]		94Homo sapiensMutation(s): 0 
Gene Names: NR1D1, EAR1, HREV, THRAL
UniProt & NIH Common Fund Data Resources
Find proteins for P20393 (Homo sapiens)
Explore P20393 
Go to UniProtKB:  P20393
PHAROS:  P20393
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20393
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
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
Protein Feature View
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  • Reference Sequence
Small Molecules
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