7K2V

PIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into Lysosomal PI(3,5)P 2 Homeostasis from a Structural-Biochemical Analysis of the PIKfyve Lipid Kinase Complex.

Lees, J.A.Li, P.Kumar, N.Weisman, L.S.Reinisch, K.M.

(2020) Mol Cell 80: 736-743.e4

  • DOI: 10.1016/j.molcel.2020.10.003
  • Primary Citation of Related Structures:  
    7K1W, 7K1Y, 7K2V

  • PubMed Abstract: 
  • The phosphoinositide PI(3,5)P 2 , generated exclusively by the PIKfyve lipid kinase complex, is key for lysosomal biology. Here, we explore how PI(3,5)P 2 levels within cells are regulated. We find the PIKfyve complex comprises five copies of the scaffolding protein Vac14 and one copy each of the lipid kinase PIKfyve, generating PI(3,5)P 2 from PI3P and the lipid phosphatase Fig4, reversing the reaction ...

    The phosphoinositide PI(3,5)P 2 , generated exclusively by the PIKfyve lipid kinase complex, is key for lysosomal biology. Here, we explore how PI(3,5)P 2 levels within cells are regulated. We find the PIKfyve complex comprises five copies of the scaffolding protein Vac14 and one copy each of the lipid kinase PIKfyve, generating PI(3,5)P 2 from PI3P and the lipid phosphatase Fig4, reversing the reaction. Fig4 is active as a lipid phosphatase in the ternary complex, whereas PIKfyve within the complex cannot access membrane-incorporated phosphoinositides due to steric constraints. We find further that the phosphoinositide-directed activities of both PIKfyve and Fig4 are regulated by protein-directed activities within the complex. PIKfyve autophosphorylation represses its lipid kinase activity and stimulates Fig4 lipid phosphatase activity. Further, Fig4 is also a protein phosphatase acting on PIKfyve to stimulate its lipid kinase activity, explaining why catalytically active Fig4 is required for maximal PI(3,5)P 2 production by PIKfyve in vivo.


    Organizational Affiliation

    Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA. Electronic address: karin.reinisch@yale.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
1-phosphatidylinositol 3-phosphate 5-kinaseA [auth P]264Homo sapiensMutation(s): 0 
Gene Names: PIKFYVEKIAA0981PIP5K3
EC: 2.7.1.150 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2I7 (Homo sapiens)
Explore Q9Y2I7 
Go to UniProtKB:  Q9Y2I7
PHAROS:  Q9Y2I7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
1-phosphatidylinositol 3-phosphate 5-kinaseB [auth A]453Homo sapiensMutation(s): 0 
Gene Names: PIKFYVEKIAA0981PIP5K3
EC: 2.7.1.150 (UniProt), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2I7 (Homo sapiens)
Explore Q9Y2I7 
Go to UniProtKB:  Q9Y2I7
PHAROS:  Q9Y2I7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131715

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2020-12-02
    Changes: Database references