Crystal structure of Hox11L1 homeodomain

Experimental Data Snapshot

  • Resolution: 1.54 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell leukemia homeobox protein 256Homo sapiensMutation(s): 0 
Gene Names: TLX2HOX11L1NCX
UniProt & NIH Common Fund Data Resources
Find proteins for O43763 (Homo sapiens)
Explore O43763 
Go to UniProtKB:  O43763
GTEx:  ENSG00000115297 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43763
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.54 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.06α = 90
b = 33.17β = 102.12
c = 34.43γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations