PDBsum entry 2rko

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Protein transport PDB id
Protein chain
280 a.a. *
* Residue conservation analysis
PDB id:
Name: Protein transport
Title: Crystal structure of the vps4p-dimer
Structure: Vacuolar protein sorting-associated protein 4. Chain: a. Fragment: aaa-atpase domain, unp residues 124-437. Synonym: vps4p, protein end13, doa4-independent degradation 6, vacuolar protein-targeting protein 10. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: vps4p. Expressed in: escherichia coli. Expression_system_taxid: 562.
3.35Å     R-factor:   0.270     R-free:   0.298
Authors: C.Hartmann,M.G.Gruetter
Key ref:
C.Hartmann et al. (2008). Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p. J Mol Biol, 377, 352-363. PubMed id: 18272179 DOI: 10.1016/j.jmb.2008.01.010
17-Oct-07     Release date:   26-Feb-08    
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Protein chain
Pfam   ArchSchema ?
P52917  (VPS4_YEAST) -  Vacuolar protein sorting-associated protein 4
437 a.a.
280 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     3 terms  


DOI no: 10.1016/j.jmb.2008.01.010 J Mol Biol 377:352-363 (2008)
PubMed id: 18272179  
Vacuolar protein sorting: two different functional states of the AAA-ATPase Vps4p.
C.Hartmann, M.Chami, U.Zachariae, Groot, A.Engel, M.G.Grütter.
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.
  Selected figure(s)  
Figure 6.
Fig. 6. ATPase activity and gel filtration of His[6]Vps4p and His[6]ΔNVps4p. The gel-filtration profiles of His[6]Vps4p and His[6]ΔNVps4p/His[6]ΔNVps4p Q216A are compared and illustrate the inability of the Q216A mutant to form dimers.
  The above figure is reprinted by permission from Elsevier: J Mol Biol (2008, 377, 352-363) copyright 2008.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20696398 D.Yang, and J.H.Hurley (2010).
Structural role of the Vps4-Vta1 interface in ESCRT-III recycling.
  Structure, 18, 976-984.
PDB code: 3mhv
20588296 J.H.Hurley, and P.I.Hanson (2010).
Membrane budding and scission by the ESCRT machinery: it's all in the neck.
  Nat Rev Mol Cell Biol, 11, 556-566.  
  20653365 J.H.Hurley (2010).
The ESCRT complexes.
  Crit Rev Biochem Mol Biol, 45, 463-487.  
20358264 M.Boone, A.Mobasheri, R.A.Fenton, B.W.van Balkom, R.Wismans, C.E.van der Zee, and P.M.Deen (2010).
The lysosomal trafficking regulator interacting protein-5 localizes mainly in epithelial cells.
  J Mol Histol, 41, 61-74.  
19535732 B.McDonald, and J.Martin-Serrano (2009).
No strings attached: the ESCRT machinery in viral budding and cytokinesis.
  J Cell Sci, 122, 2167-2177.  
19699748 J.D.Batchelor, H.J.Sterling, E.Hong, E.R.Williams, and D.E.Wemmer (2009).
Receiver domains control the active-state stoichiometry of Aquifex aeolicus sigma54 activator NtrC4, as revealed by electrospray ionization mass spectrometry.
  J Mol Biol, 393, 634-643.  
19129479 M.Bajorek, E.Morita, J.J.Skalicky, S.G.Morham, M.Babst, and W.I.Sundquist (2009).
Biochemical analyses of human IST1 and its function in cytokinesis.
  Mol Biol Cell, 20, 1360-1373.  
19278657 M.J.Landsberg, P.R.Vajjhala, R.Rothnagel, A.L.Munn, and B.Hankamer (2009).
Three-dimensional structure of AAA ATPase Vps4: advancing structural insights into the mechanisms of endosomal sorting and enveloped virus budding.
  Structure, 17, 427-437.  
18929572 M.D.Gonciarz, F.G.Whitby, D.M.Eckert, C.Kieffer, A.Heroux, W.I.Sundquist, and C.P.Hill (2008).
Biochemical and structural studies of yeast Vps4 oligomerization.
  J Mol Biol, 384, 878-895.
PDB codes: 3eie 3eih
18786397 S.Ghazi-Tabatabai, S.Saksena, J.M.Short, A.V.Pobbati, D.B.Veprintsev, R.A.Crowther, S.D.Emr, E.H.Egelman, and R.L.Williams (2008).
Structure and disassembly of filaments formed by the ESCRT-III subunit Vps24.
  Structure, 16, 1345-1356.  
18385515 S.Shim, S.A.Merrill, and P.I.Hanson (2008).
Novel interactions of ESCRT-III with LIP5 and VPS4 and their implications for ESCRT-III disassembly.
  Mol Biol Cell, 19, 2661-2672.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.