5DFZ

Structure of Vps34 complex II from S. cerevisiae.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.40 Å
  • R-Value Free: 0.376 
  • R-Value Work: 0.368 
  • R-Value Observed: 0.369 

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This is version 1.2 of the entry. See complete history


Literature

Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes.

Rostislavleva, K.Soler, N.Ohashi, Y.Zhang, L.Pardon, E.Burke, J.E.Masson, G.R.Johnson, C.Steyaert, J.Ktistakis, N.T.Williams, R.L.

(2015) Science 350: aac7365-aac7365

  • DOI: 10.1126/science.aac7365
  • Primary Citation of Related Structures:  
    5DFZ

  • PubMed Abstract: 
  • Phosphatidylinositol 3-kinase Vps34 complexes regulate intracellular membrane trafficking in endocytic sorting, cytokinesis, and autophagy. We present the 4.4 angstrom crystal structure of the 385-kilodalton endosomal complex II (PIK3C3-CII), consist ...

    Phosphatidylinositol 3-kinase Vps34 complexes regulate intracellular membrane trafficking in endocytic sorting, cytokinesis, and autophagy. We present the 4.4 angstrom crystal structure of the 385-kilodalton endosomal complex II (PIK3C3-CII), consisting of Vps34, Vps15 (p150), Vps30/Atg6 (Beclin 1), and Vps38 (UVRAG). The subunits form a Y-shaped complex, centered on the Vps34 C2 domain. Vps34 and Vps15 intertwine in one arm, where the Vps15 kinase domain engages the Vps34 activation loop to regulate its activity. Vps30 and Vps38 form the other arm that brackets the Vps15/Vps34 heterodimer, suggesting a path for complex assembly. We used hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal conformational changes accompanying membrane binding and identify a Vps30 loop that is critical for the ability of complex II to phosphorylate giant liposomes on which complex I is inactive.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 38A441Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS38VPL17YLR360WL8039.11
Find proteins for Q05919 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q05919
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase VPS34C875Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS34END12PEP15VPL7VPT29YLR240WL9672.10
EC: 2.7.1.137
Find proteins for P22543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase VPS15B1460Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS15GRD8VAC4VPL19YBR097WYBR0825
EC: 2.7.11.1
Find proteins for P22219 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody binding S. cerevisiae Vps34E124Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 30D559Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: VPS30APG6ATG6VPT30YPL120WLPH7
Find proteins for Q02948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q02948
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Putative N-terminal domain of S. cerevisiae Vps30G49Saccharomyces cerevisiaeMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.40 Å
  • R-Value Free: 0.376 
  • R-Value Work: 0.368 
  • R-Value Observed: 0.369 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 215.18α = 90
b = 226.84β = 90
c = 127.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
SHARPphasing
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cambridge Cancer Center PhD fellowshipUnited Kingdom--
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K019155/1
Medical Research Council (United Kingdom)United KingdomU105184308

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Advisory, Author supporting evidence, Derived calculations