3NS4

Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of GARP to a family of tethering complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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Literature

Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of Golgi-associated retrograde protein (GARP) complex to a family of tethering complexes.

Vasan, N.Hutagalung, A.Novick, P.Reinisch, K.M.

(2010) Proc Natl Acad Sci U S A 107: 14176-14181

  • DOI: 10.1073/pnas.1009419107
  • Primary Citation of Related Structures:  
    3NS4

  • PubMed Abstract: 
  • The Golgi-associated retrograde protein (GARP) complex is a membrane-tethering complex that functions in traffic from endosomes to the trans-Golgi network. Here we present the structure of a C-terminal fragment of the Vps53 subunit, important for binding endosome-derived vesicles, at a resolution of 2 ...

    The Golgi-associated retrograde protein (GARP) complex is a membrane-tethering complex that functions in traffic from endosomes to the trans-Golgi network. Here we present the structure of a C-terminal fragment of the Vps53 subunit, important for binding endosome-derived vesicles, at a resolution of 2.9 A. We show that the C terminus consists of two alpha-helical bundles arranged in tandem, and we identify a highly conserved surface patch, which may play a role in vesicle recognition. Mutations of the surface result in defects in membrane traffic. The fold of the Vps53 C terminus is strongly reminiscent of proteins that belong to three other tethering complexes--Dsl1, conserved oligomeric Golgi, and the exocyst--thought to share a common evolutionary origin. Thus, the structure of the Vps53 C terminus suggests that GARP belongs to this family of complexes.


    Organizational Affiliation

    Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 53A271Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: VPS53YJL029CJ1258
UniProt
Find proteins for P47061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47061 
Go to UniProtKB:  P47061
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BA
Query on BA

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.236α = 90
b = 127.236β = 90
c = 81.658γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
REFMACrefinement
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: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance