2RKO

Crystal Structure of the Vps4p-dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p

Hartmann, C.Chami, M.Zachariae, U.de Groot, B.L.Engel, A.Gruetter, M.G.

(2008) J.Mol.Biol. 377: 352-363

  • DOI: 10.1016/j.jmb.2008.01.010

  • PubMed Abstract: 
  • The vacuolar protein sorting (Vps) pathway, in which Vps4 class I AAA-ATPases play a central role, regulates growth factor receptors, immune response, and developmental signaling, and participates in tumor suppression, apoptosis, and retrovirus buddi ...

    The vacuolar protein sorting (Vps) pathway, in which Vps4 class I AAA-ATPases play a central role, regulates growth factor receptors, immune response, and developmental signaling, and participates in tumor suppression, apoptosis, and retrovirus budding. We present the first atomic structure of the nucleotide-free yeast His(6)DeltaNVps4p dimer and its AMPPNP (5'-adenylyl-beta,gamma-imidodiphosphate)-bound tetradecamer, derived from a cryo electron microscopy map. Vps4p dimers form two distinct heptameric rings and accommodate AAA cassettes in a head-to-head--not in a head-to-tail-fashion as in class II AAA-ATPases. Our model suggests a mechanism for disassembling ESCRT (endosomal sorting complex required for transport) complexes by movements of substrate-binding domains located at the periphery of the tetradecamer during ATP hydrolysis in one ring, followed by translocation through the central pore and ATP hydrolysis in the second ring.


    Organizational Affiliation

    Institute of Biochemistry, University of Zürich, Winterthurer Strasse 190, 8057 Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 4
A
331Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPS4 (CSC1, DID6, END13, GRD13, VPL4, VPT10)
Find proteins for P52917 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P52917
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.268 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 109.116α = 90.00
b = 109.116β = 90.00
c = 176.632γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance