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- PDB-7k2v: PIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2 -

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Basic information

Entry
Database: PDB / ID: 7k2v
TitlePIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2
Components(1-phosphatidylinositol 3-phosphate 5-kinase) x 2
KeywordsLIPID BINDING PROTEIN / Lipid kinase / Lipid phosphatase / protein complex
Function / homology
Function and homology information


1-phosphatidylinositol-3-phosphate 5-kinase / 1-phosphatidylinositol-3-phosphate 5-kinase activity / 1-phosphatidylinositol-5-kinase activity / phosphatidylinositol 5-phosphate metabolic process / 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / myelin assembly / Synthesis of PIPs at the late endosome membrane / phagosome-lysosome fusion / Synthesis of PIPs at the early endosome membrane ...1-phosphatidylinositol-3-phosphate 5-kinase / 1-phosphatidylinositol-3-phosphate 5-kinase activity / 1-phosphatidylinositol-5-kinase activity / phosphatidylinositol 5-phosphate metabolic process / 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate metabolic process / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / myelin assembly / Synthesis of PIPs at the late endosome membrane / phagosome-lysosome fusion / Synthesis of PIPs at the early endosome membrane / 1-phosphatidylinositol-4-phosphate 5-kinase activity / phagosome maturation / Synthesis of PIPs at the Golgi membrane / peptidyl-serine autophosphorylation / melanosome organization / regulation of autophagosome assembly / phosphatidylinositol biosynthetic process / retrograde transport, endosome to Golgi / regulation of reactive oxygen species biosynthetic process / protein targeting to membrane / vesicle membrane / protein localization to nucleus / neutrophil chemotaxis / phagocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / cell-cell junction / late endosome membrane / early endosome membrane / cytoplasmic vesicle / receptor-mediated endocytosis of virus by host cell / non-specific serine/threonine protein kinase / endosome membrane / intracellular signal transduction / membrane raft / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / zinc ion binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
PIKfyve, DEP domain / 1-phosphatidylinositol-3phosphate-5-kinase / 1-phosphatidylinositol-3-phosphate 5-kinase, PIPK catalytic domain / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Phosphatidylinositol-4-phosphate 5-kinase, core / : / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase ...PIKfyve, DEP domain / 1-phosphatidylinositol-3phosphate-5-kinase / 1-phosphatidylinositol-3-phosphate 5-kinase, PIPK catalytic domain / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Phosphatidylinositol-4-phosphate 5-kinase, core / : / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Phosphoinositide kinase, FYVE-type zinc finger containing / 1-phosphatidylinositol 3-phosphate 5-kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsLees, J.A. / Reinisch, K.M. / Li, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131715 United States
CitationJournal: Mol Cell / Year: 2020
Title: Insights into Lysosomal PI(3,5)P Homeostasis from a Structural-Biochemical Analysis of the PIKfyve Lipid Kinase Complex.
Authors: Joshua A Lees / PeiQi Li / Nikit Kumar / Lois S Weisman / Karin M Reinisch /
Abstract: The phosphoinositide PI(3,5)P, generated exclusively by the PIKfyve lipid kinase complex, is key for lysosomal biology. Here, we explore how PI(3,5)P levels within cells are regulated. We find the ...The phosphoinositide PI(3,5)P, generated exclusively by the PIKfyve lipid kinase complex, is key for lysosomal biology. Here, we explore how PI(3,5)P 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 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 production by PIKfyve in vivo.
History
DepositionSep 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
P: 1-phosphatidylinositol 3-phosphate 5-kinase
A: 1-phosphatidylinositol 3-phosphate 5-kinase


Theoretical massNumber of molelcules
Total (without water)81,8762
Polymers81,8762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area280 Å2
ΔGint-1 kcal/mol
Surface area42540 Å2

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Components

#1: Protein 1-phosphatidylinositol 3-phosphate 5-kinase / Phosphatidylinositol 3-phosphate 5-kinase / FYVE finger-containing phosphoinositide kinase / ...Phosphatidylinositol 3-phosphate 5-kinase / FYVE finger-containing phosphoinositide kinase / PIKfyve / Phosphatidylinositol 3-phosphate 5-kinase type III / Type III PIP kinase


Mass: 30462.967 Da / Num. of mol.: 1 / Fragment: PIPK domain (UNP residues 1822-2085)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIKFYVE, KIAA0981, PIP5K3 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
References: UniProt: Q9Y2I7, 1-phosphatidylinositol-3-phosphate 5-kinase
#2: Protein 1-phosphatidylinositol 3-phosphate 5-kinase


Mass: 51413.039 Da / Num. of mol.: 1 / Fragment: CCT domain (UNP residues 491-927)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIKFYVE / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: E9PDH4, UniProt: Q9Y2I7*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PIKfyve/Fig4/Vac14 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 4.28 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingElectron dose: 58.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19998 / Symmetry type: POINT

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