1WRD

Crystal structure of Tom1 GAT domain in complex with ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.

Akutsu, M., Kawasaki, M., Katoh, Y., Shiba, T., Yamaguchi, Y., Kato, R., Kato, K., Nakayama, K., Wakatsuki, S.

(2005) FEBS Lett 579: 5385-5391

  • DOI: 10.1016/j.febslet.2005.08.076
  • Primary Citation of Related Structures:  
    1WRD

  • PubMed Abstract: 

    • Tom1 (Target of Myb1) is suggested to be involved in the transport of ubiquitinated proteins, through the interaction of its GAT (GGA and Tom1) domain with ubiquitin. Here, we demonstrate that the three-helix bundle of Tom1-GAT has two ubiquitin-binding ...

    Tom1 (Target of Myb1) is suggested to be involved in the transport of ubiquitinated proteins, through the interaction of its GAT (GGA and Tom1) domain with ubiquitin. Here, we demonstrate that the three-helix bundle of Tom1-GAT has two ubiquitin-binding sites recognizing the hydrophobic Ile44 surface of ubiquitin. The complex crystal structure demonstrates that the first site is a hydrophobic patch on helices alpha1 and alpha2. NMR and biochemical data revealed that the N-terminal half of helix alpha3 of Tom1-GAT constitutes the second, stronger binding site. The double-sided ubiquitin binding enhances the efficiency of recognition of ubiquitinated proteins by Tom1.

    Organizational Affiliation: 

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Target of Myb protein 1 A103Homo sapiensMutation(s): 0 
Gene Names: TOM1
Find proteins for O60784 (Homo sapiens)
Explore O60784 
Go to UniProtKB:  O60784
NIH Common Fund Data Resources
PHAROS:  O60784
GTEx:  ENSG00000100284
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin B76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P0CH28 (Bos taurus)
Explore P0CH28 
Go to UniProtKB:  P0CH28
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.317α = 90
b = 168.317β = 90
c = 168.317γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance