2YMA

X-ray structure of the Yos9 dimerization domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Biochemical Basis of Yos9 Protein Dimerization and Possible Contribution to Self-Association of 3-Hydroxy-3-Methylglutaryl-Coenzyme a Reductase Degradation Ubiquitin-Ligase Complex.

Hanna, J.Schutz, A.Zimmermann, F.Behlke, J.Sommer, T.Heinemann, U.

(2012) J Biol Chem 287: 8633

  • DOI: 10.1074/jbc.M111.317644
  • Primary Citation of Related Structures:  
    2YMA

  • PubMed Abstract: 
  • In yeast, the membrane-bound HMG-CoA reductase degradation (HRD) ubiquitin-ligase complex is a key player of the ER-associated protein degradation pathway that targets misfolded proteins for proteolysis. Yos9, a component of the luminal submodule of the ...

    In yeast, the membrane-bound HMG-CoA reductase degradation (HRD) ubiquitin-ligase complex is a key player of the ER-associated protein degradation pathway that targets misfolded proteins for proteolysis. Yos9, a component of the luminal submodule of the ligase, scans proteins for specific oligosaccharide modifications, which constitute a critical determinant of the degradation signal. Here, we report the crystal structure of the Yos9 domain that was previously suggested to confer binding to Hrd3, another component of the HRD complex. We observe an αβ-roll domain architecture and a dimeric assembly which are confirmed by analytical ultracentrifugation of both the crystallized domain and full-length Yos9. Our binding studies indicate that, instead of this domain, the N-terminal part of Yos9 including the mannose 6-phosphate receptor homology domain mediates the association with Hrd3 in vitro. Our results support the model of a dimeric state of the HRD complex and provide first-time evidence of self-association on its luminal side.


    Organizational Affiliation

    Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN OS-9 HOMOLOG AB161Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q99220 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99220 
Go to UniProtKB:  Q99220
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.8α = 90
b = 160.8β = 90
c = 97.66γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Other