Crystal Structure of Yeast Vps74

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.237 

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Golgi localization of glycosyltransferases requires a Vps74p oligomer.

Schmitz, K.R.Liu, J.Li, S.Setty, T.G.Wood, C.S.Burd, C.G.Ferguson, K.M.

(2008) Dev Cell 14: 523-534

  • DOI: https://doi.org/10.1016/j.devcel.2008.02.016
  • Primary Citation of Related Structures:  
    2ZIH, 2ZII

  • PubMed Abstract: 

    The mechanism of glycosyltransferase localization to the Golgi apparatus is a long-standing question in secretory cell biology. All Golgi glycosyltransferases are type II membrane proteins with small cytosolic domains that contribute to Golgi localization. To date, no protein has been identified that recognizes the cytosolic domains of Golgi enzymes and contributes to their localization. Here, we report that yeast Vps74p directly binds to the cytosolic domains of cis and medial Golgi mannosyltransferases and that loss of this interaction correlates with loss of Golgi localization of these enzymes. We have solved the X-ray crystal structure of Vps74p and find that it forms a tetramer, which we also observe in solution. Deletion of a critical structural motif disrupts tetramer formation and results in loss of Vps74p localization and function. Vps74p is highly homologous to the human GMx33 Golgi matrix proteins, suggesting a conserved function for these proteins in the Golgi enzyme localization machinery.

  • Organizational Affiliation

    Department of Physiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 74
A, B, C, D
347Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS74
Find proteins for Q06385 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06385 
Go to UniProtKB:  Q06385
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06385
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.237 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.688α = 90
b = 102.688β = 90
c = 292.323γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description