1C20

SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN FROM THE DEAD RINGER PROTEIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 21 
  • Selection Criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, WITH FAVORABLE NON-BOND ENERGY, AND WITH THE LEAST RESTRAINT VIOLATIONS. 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID).

Iwahara, J.Clubb, R.T.

(1999) EMBO J 18: 6084-6094

  • DOI: 10.1093/emboj/18.21.6084
  • Primary Citation of Related Structures:  
    1C20

  • PubMed Abstract: 
  • The Dead ringer protein from Drosophila melanogaster is a transcriptional regulatory protein required for early embryonic development. It is the founding member of a large family of DNA binding proteins that interact with DNA through a highly conserved domain called the AT-rich interaction domain (ARID) ...

    The Dead ringer protein from Drosophila melanogaster is a transcriptional regulatory protein required for early embryonic development. It is the founding member of a large family of DNA binding proteins that interact with DNA through a highly conserved domain called the AT-rich interaction domain (ARID). The solution structure of the Dead ringer ARID (residues Gly262-Gly398) was determined using NMR spectroscopy. The ARID forms a unique globular structure consisting of eight alpha-helices and a short two-stranded anti-parallel beta-sheet. Amino acid sequence homology indicates that ARID DNA binding proteins are partitioned into three structural classes: (i) minimal ARID proteins that consist of a core domain formed by six alpha-helices; (ii) ARID proteins that supplement the core domain with an N-terminal alpha-helix; and (iii) extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. Studies of the Dead ringer-DNA complex suggest that the major groove of DNA is recognized by a helix-turn-helix (HTH) motif and the adjacent minor grooves are contacted by a beta-hairpin and C-terminal alpha-helix. Primary homology suggests that all ARID-containing proteins contact DNA through the HTH and hairpin structures, but only extended-ARID proteins supplement this binding surface with a terminal helix.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Molecular Biology Institute and the UCLA-DOE Laboratory of Structural Biology and Genetics, University of California, Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095-1570, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEAD RINGER PROTEINA128Drosophila melanogasterMutation(s): 0 
Gene Names: retndriCG5403
UniProt
Find proteins for Q24573 (Drosophila melanogaster)
Explore Q24573 
Go to UniProtKB:  Q24573
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 21 
  • Selection Criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, WITH FAVORABLE NON-BOND ENERGY, AND WITH THE LEAST RESTRAINT VIOLATIONS. 
  • OLDERADO: 1C20 Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance