PIKfyve/Fig4/Vac14 complex centered on Fig4 - map3

Experimental Data Snapshot

  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fig4 Sac homology modelA [auth F]918Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q92562 (Homo sapiens)
Explore Q92562 
Go to UniProtKB:  Q92562
PHAROS:  Q92562
GTEx:  ENSG00000112367 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92562
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

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
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references