3LNQ

Structure of Aristaless homeodomain in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless

Miyazono, K.Zhi, Y.Takamura, Y.Nagata, K.Saigo, K.Kojima, T.Tanokura, M.

(2010) EMBO J 29: 1613-1623

  • DOI: 10.1038/emboj.2010.53
  • Primary Citation of Related Structures:  
    3A01, 3A02, 3A03, 3LNQ

  • PubMed Abstract: 
  • To achieve accurate gene regulation, some homeodomain proteins bind cooperatively to DNA to increase those site specificities. We report a ternary complex structure containing two homeodomain proteins, aristaless (Al) and clawless (Cll), bound to DNA. Our results show that the extended conserved sequences of the Cll homeodomain are indispensable to cooperative DNA binding ...

    To achieve accurate gene regulation, some homeodomain proteins bind cooperatively to DNA to increase those site specificities. We report a ternary complex structure containing two homeodomain proteins, aristaless (Al) and clawless (Cll), bound to DNA. Our results show that the extended conserved sequences of the Cll homeodomain are indispensable to cooperative DNA binding. In the Al-Cll-DNA complex structure, the residues in the extended regions are used not only for the intermolecular contacts between the two homeodomain proteins but also for the sequence-recognition mechanism of DNA by direct interactions. The residues in the extended N-terminal arm lie within the minor groove of DNA to form direct interactions with bases, whereas the extended conserved region of the C-terminus of the homeodomain interacts with Al to stabilize and localize the third alpha helix of the Cll homeodomain. This structure suggests a novel mode for the cooperativity of homeodomain proteins.


    Organizational Affiliation

    Department of Applied Biological Chemistry, University of Tokyo, Bunkyo-ku, Tokyo, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homeobox protein aristalessA58Drosophila melanogasterMutation(s): 0 
Gene Names: alCG3935
UniProt
Find proteins for Q06453 (Drosophila melanogaster)
Explore Q06453 
Go to UniProtKB:  Q06453
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*TP*TP*TP*AP*AP*TP*TP*AP*GP*GP*G)-3'B14N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*CP*CP*TP*AP*AP*TP*TP*AP*AP*AP*CP*CP*C)-3'C14N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ACT
      Query on ACT

      Download Ideal Coordinates CCD File 
      D [auth B]ACETATE ION
      C2 H3 O2
      QTBSBXVTEAMEQO-UHFFFAOYSA-M
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.25 Å
      • R-Value Free: 0.251 
      • R-Value Work: 0.227 
      • R-Value Observed: 0.228 
      • Space Group: P 43 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 42.35α = 90
      b = 42.35β = 90
      c = 162.73γ = 90
      Software Package:
      Software NamePurpose
      XSCALEdata scaling
      REFMACrefinement
      PDB_EXTRACTdata extraction
      XDSdata reduction
      MOLREPphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2010-04-28
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance