3A03

Crystal structure of Hox11L1 homeodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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
T-cell leukemia homeobox protein 2A56Homo sapiensMutation(s): 0 
Gene Names: TLX2HOX11L1NCX
UniProt & NIH Common Fund Data Resources
Find proteins for O43763 (Homo sapiens)
Explore O43763 
Go to UniProtKB:  O43763
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
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