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 1.3 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: https://doi.org/10.1093/emboj/21.5.1197
  • Primary Citation of Related Structures:  
    1KQQ

  • 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 Dead ringer from Drosophila melanogaster ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DEAD RINGER PROTEINC [auth A]139Drosophila melanogasterMutation(s): 1 
Gene Names: dri, retn, CG5403
UniProt
Find proteins for Q24573 (Drosophila melanogaster)
Explore Q24573 
Go to UniProtKB:  Q24573
Entity Groups  
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UniProt GroupQ24573
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3'A [auth B]15N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3'B [auth C]15N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DNA PDBBind:  1KQQ Kd: 28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Data collection, Database references, Derived calculations