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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22647 | |||||||||
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Title | PIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2 | |||||||||
![]() | PIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2 | |||||||||
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![]() | Lipid kinase / Lipid phosphatase / protein complex / LIPID BINDING PROTEIN | |||||||||
Function / homology | ![]() 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 / myelin assembly / Synthesis of PIPs at the late endosome membrane / protein serine/threonine kinase activity => GO:0004674 / Synthesis of PIPs at the early endosome membrane / 1-phosphatidylinositol-4-phosphate 5-kinase activity ...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 / myelin assembly / Synthesis of PIPs at the late endosome membrane / protein serine/threonine kinase activity => GO:0004674 / Synthesis of PIPs at the early endosome membrane / 1-phosphatidylinositol-4-phosphate 5-kinase activity / phagosome-lysosome fusion / phagosome maturation / Synthesis of PIPs at the Golgi membrane / regulation of autophagosome assembly / peptidyl-serine autophosphorylation / melanosome organization / phosphatidylinositol biosynthetic process / retrograde transport, endosome to Golgi / regulation of reactive oxygen species biosynthetic process / protein targeting to 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 / receptor-mediated endocytosis of virus by host cell / non-specific serine/threonine protein kinase / endosome membrane / intracellular signal transduction / membrane raft / Golgi membrane / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / ATP hydrolysis activity / zinc ion binding / ATP binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
![]() | Lees JA / Reinisch KM | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 226 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.4 KB 11.4 KB | Display Display | ![]() |
Images | ![]() | 57.3 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 486 KB | Display | ![]() |
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Full document | ![]() | 485.5 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k2vMC ![]() 7k1wC ![]() 7k1yC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | PIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : PIKfyve/Fig4/Vac14 complex
Entire | Name: PIKfyve/Fig4/Vac14 complex |
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Components |
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-Supramolecule #1: PIKfyve/Fig4/Vac14 complex
Supramolecule | Name: PIKfyve/Fig4/Vac14 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.28 MDa |
-Macromolecule #1: 1-phosphatidylinositol 3-phosphate 5-kinase
Macromolecule | Name: 1-phosphatidylinositol 3-phosphate 5-kinase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: 1-phosphatidylinositol-3-phosphate 5-kinase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.462967 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: CRLYYAGEFH KMREVILDSS EEDFIRSLSH SSPWQARGGK SGAAFYATED DRFILKQMPR LEVQSFLDFA PHYFNYITNA VQQKRPTAL AKILGVYRIG YKNSQNNTEK KLDLLVMENL FYGRKMAQVF DLKGSLRNRN VKTDTGKESC DVVLLDENLL K MVRDNPLY ...String: CRLYYAGEFH KMREVILDSS EEDFIRSLSH SSPWQARGGK SGAAFYATED DRFILKQMPR LEVQSFLDFA PHYFNYITNA VQQKRPTAL AKILGVYRIG YKNSQNNTEK KLDLLVMENL FYGRKMAQVF DLKGSLRNRN VKTDTGKESC DVVLLDENLL K MVRDNPLY IRSHSKAVLR TSIHSDSHFL SSHLIIDYSL LVGRDDTSNE LVVGIIDYIR TFTWDKKLEM VVKSTGILGG QG KMPTVVS PELYRTRFCE AMDKYFL UniProtKB: 1-phosphatidylinositol 3-phosphate 5-kinase |
-Macromolecule #2: 1-phosphatidylinositol 3-phosphate 5-kinase
Macromolecule | Name: 1-phosphatidylinositol 3-phosphate 5-kinase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 51.413039 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SSFQSTVDSD SADQKEYLIS DTGGQQLSIS DAFIKESLFN RRVEEKSKEL PFTPLGWHHN NLELLREENG EKQAMERLLS ANHNHMMAL LQQLLHSDSL SSSWRDIIVS LVCQVVQTVR PDVKNQDDDM DIRQFVHIKK IPGGKKFDSV VVNGFVCTKN I AHKKMSSC ...String: SSFQSTVDSD SADQKEYLIS DTGGQQLSIS DAFIKESLFN RRVEEKSKEL PFTPLGWHHN NLELLREENG EKQAMERLLS ANHNHMMAL LQQLLHSDSL SSSWRDIIVS LVCQVVQTVR PDVKNQDDDM DIRQFVHIKK IPGGKKFDSV VVNGFVCTKN I AHKKMSSC IKNPKILLLK CSIEYLYREE TKFTCIDPIV LQEREFLKNY VQRIVDVRPT LVLVEKTVSR IAQDMLLEHG IT LVINVKS QVLERISRMT QGDLVMSMDQ LLTKPHLGTC HKFYMQIFQL PNEQTKTLMF FEGCPQHLGC TIKLRGGSDY ELA RVKEIL IFMICVAYHS QLEISFLMDE FAMPPTLMQN PSFHSLIEGR GHEGAVQEQY GGGSIPWDPD IPPESLPCDD SSLL ELRIV FEKGEQENKN LPQAVASVKH QEHSTTACPA GLPCAFFAPV PESLLPLP UniProtKB: 1-phosphatidylinositol 3-phosphate 5-kinase |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 58.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19998 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |