5KC2

Negative stain structure of Vps15/Vps34 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 28.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex.

Ohashi, Y.Soler, N.Garcia Ortegon, M.Zhang, L.Kirsten, M.L.Perisic, O.Masson, G.R.Burke, J.E.Jakobi, A.J.Apostolakis, A.A.Johnson, C.M.Ohashi, M.Ktistakis, N.T.Sachse, C.Williams, R.L.

(2016) Autophagy 12: 2129-2144

  • DOI: 10.1080/15548627.2016.1226736
  • Primary Citation of Related Structures:  
    5KC2, 5KC1

  • PubMed Abstract: 
  • The phosphatidylinositol 3-kinase Vps34 is part of several protein complexes. The structural organization of heterotetrameric complexes is starting to emerge, but little is known about organization of additional accessory subunits that interact with ...

    The phosphatidylinositol 3-kinase Vps34 is part of several protein complexes. The structural organization of heterotetrameric complexes is starting to emerge, but little is known about organization of additional accessory subunits that interact with these assemblies. Combining hydrogen-deuterium exchange mass spectrometry (HDX-MS), X-ray crystallography and electron microscopy (EM), we have characterized Atg38 and its human ortholog NRBF2, accessory components of complex I consisting of Vps15-Vps34-Vps30/Atg6-Atg14 (yeast) and PIK3R4/VPS15-PIK3C3/VPS34-BECN1/Beclin 1-ATG14 (human). HDX-MS shows that Atg38 binds the Vps30-Atg14 subcomplex of complex I, using mainly its N-terminal MIT domain and bridges the coiled-coil I regions of Atg14 and Vps30 in the base of complex I. The Atg38 C-terminal domain is important for localization to the phagophore assembly site (PAS) and homodimerization. Our 2.2 Å resolution crystal structure of the Atg38 C-terminal homodimerization domain shows 2 segments of α-helices assembling into a mushroom-like asymmetric homodimer with a 4-helix cap and a parallel coiled-coil stalk. One Atg38 homodimer engages a single complex I. This is in sharp contrast to human NRBF2, which also forms a homodimer, but this homodimer can bridge 2 complex I assemblies.


    Organizational Affiliation

    a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase VPS34C875Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS34END12PEP15VPL7VPT29YLR240WL9672.10
EC: 2.7.1.137
Find proteins for P22543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22543 
Go to UniProtKB:  P22543
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase VPS15B1454Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS15GRD8VAC4VPL19YBR097WYBR0825
EC: 2.7.11.1
Find proteins for P22219 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22219 
Go to UniProtKB:  P22219
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 28.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2016-11-09
    Changes: Database references
  • Version 1.3: 2017-07-26
    Changes: Experimental preparation
  • Version 1.4: 2017-08-02
    Changes: Data collection
  • Version 1.5: 2019-10-23
    Changes: Data collection, Other
  • Version 1.6: 2019-11-13
    Changes: Data collection, Other