1KQQ

Solution Structure of the Dead ringer ARID-DNA Complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA.

Iwahara, J.Iwahara, M.Daughdrill, G.W.Ford, J.Clubb, R.T.

(2002) EMBO J. 21: 1197-1209

  • DOI: 10.1093/emboj/21.5.1197

  • PubMed Abstract: 
  • The AT-rich interaction domain (ARID) is a DNA-binding module found in many eukaryotic transcription factors. Using NMR spectroscopy, we have determined the first ever three-dimensional structure of an ARID--DNA complex (mol. wt 25.7 kDa) formed by D ...

    The AT-rich interaction domain (ARID) is a DNA-binding module found in many eukaryotic transcription factors. Using NMR spectroscopy, we have determined the first ever three-dimensional structure of an ARID--DNA complex (mol. wt 25.7 kDa) formed by Dead ringer from Drosophila melanogaster. ARIDs recognize DNA through a novel mechanism involving major groove immobilization of a large loop that connects the helices of a non-canonical helix-turn-helix motif, and through a concomitant structural rearrangement that produces stabilizing contacts from a beta-hairpin. Dead ringer's preference for AT-rich DNA originates from three positions within the ARID fold that form energetically significant contacts to an adenine-thymine base step. Amino acids that dictate binding specificity are not highly conserved, suggesting that ARIDs will bind to a range of nucleotide sequences. Extended ARIDs, found in several sequence-specific transcription factors, are distinguished by the presence of a C-terminal helix that may increase their intrinsic affinity for DNA. The prevalence of serine amino acids at all specificity determining positions suggests that ARIDs within SWI/SNF-related complexes will interact with DNA non-sequence specifically.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DEAD RINGER PROTEIN
A
139Drosophila melanogasterMutations: F96L
Gene Names: retn (dri)
Find proteins for Q24573 (Drosophila melanogaster)
Go to UniProtKB:  Q24573
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3'B15N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3'C15N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 1KQQ Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance