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- PDB-7k1w: PIKfyve/Fig4/Vac14 complex centered on Fig4 - map3 -

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Basic information

Entry
Database: PDB / ID: 7k1w
TitlePIKfyve/Fig4/Vac14 complex centered on Fig4 - map3
ComponentsFig4 Sac homology model
KeywordsLIPID BINDING PROTEIN / Lipid kinase / Lipid phosphatase / protein complex
Function / homology
Function and homology information


phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol dephosphorylation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatidylinositol biosynthetic process / lipid droplet / late endosome membrane / early endosome membrane ...phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol dephosphorylation / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatidylinositol biosynthetic process / lipid droplet / late endosome membrane / early endosome membrane / endosome membrane / Golgi membrane / intracellular membrane-bounded organelle
Similarity search - Function
Polyphosphoinositide phosphatase Fig4-like / SAC domain / SacI homology domain / Sac phosphatase domain profile.
Similarity search - Domain/homology
Polyphosphoinositide phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 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 8, 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
F: Fig4 Sac homology model


Theoretical massNumber of molelcules
Total (without water)105,1441
Polymers105,1441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24880 Å2

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Components

#1: Protein Fig4 Sac homology model


Mass: 105144.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q92562*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 FIELDBright-field microscopy / 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

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19998 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0073805
ELECTRON MICROSCOPYf_angle_d1.185155
ELECTRON MICROSCOPYf_dihedral_angle_d6.0872273
ELECTRON MICROSCOPYf_chiral_restr0.059574
ELECTRON MICROSCOPYf_plane_restr0.008657

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