1WMG

Crystal structure of the UNC5H2 death domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of the UNC5H2 death domain

Handa, N., Kukimoto-Niino, M., Akasaka, R., Murayama, K., Terada, T., Inoue, M., Yabuki, T., Aoki, M., Seki, E., Matsuda, T., Nunokawa, E., Tanaka, A., Hayashizaki, Y., Kigawa, T., Shirouzu, M., Yokoyama, S.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1502-1509

  • DOI: 10.1107/S0907444906039369
  • Primary Citation of Related Structures:  
    1WMG

  • PubMed Abstract: 

    • UNC5Hs (UNC5H1-4) are netrin 1 receptors that are involved in axonal guidance and neuronal migration. They are dependence receptors that mediate apoptosis in the absence of netrin 1. UNC5H2-induced apoptosis depends on the interaction of the death domain ...

    UNC5Hs (UNC5H1-4) are netrin 1 receptors that are involved in axonal guidance and neuronal migration. They are dependence receptors that mediate apoptosis in the absence of netrin 1. UNC5H2-induced apoptosis depends on the interaction of the death domain at the C-terminus with the DAP-kinase death domain and caspase cleavage near the transmembrane region. Here, the crystal structure of the mouse UNC5H2 death domain has been determined at 2.1 A resolution. The domain adopts a six-helix bundle fold, which is similar to those of the other members of the death-domain superfamily. The UNC5H2 death domain is a dimer in the crystal and in solution. This homodimerized structure may represent the structure of the death domain when netrin 1 binds to the UNC5H2 receptor. Homodimerization of UNC5H2 may block the access of caspase to the cleavage site. In the death-domain dimer, residues in alpha3 and the 3(10)-helix preceding alpha3 and the residues in alpha4 make significant contacts, mainly by hydrophobic and van der Waals interactions.

    Organizational Affiliation: 

    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
netrin receptor Unc5h2 A, B, C, D, E, F103Mus musculusMutation(s): 4 
Gene Names: Unc5b, Unc5h2
Find proteins for Q8K1S3 (Mus musculus)
Explore Q8K1S3 
Go to UniProtKB:  Q8K1S3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.878α = 90
b = 47.207β = 119.56
c = 121.177γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model