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- EMDB-22647: PIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2 -

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Basic information

Entry
Database: EMDB / ID: EMD-22647
TitlePIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2
Map dataPIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2
Sample
  • Complex: PIKfyve/Fig4/Vac14 complex
    • Protein or peptide: 1-phosphatidylinositol 3-phosphate 5-kinase
    • Protein or peptide: 1-phosphatidylinositol 3-phosphate 5-kinase
KeywordsLipid kinase / Lipid phosphatase / protein complex / LIPID BINDING PROTEIN
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 / 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 / phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / myelin assembly / Synthesis of PIPs at the late endosome membrane / phagosome-lysosome fusion / 1-phosphatidylinositol-4-phosphate 5-kinase activity / Synthesis of PIPs at the early endosome membrane / phagosome maturation / Synthesis of PIPs at the Golgi membrane / peptidyl-serine autophosphorylation / regulation of autophagosome assembly / melanosome organization / 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 / receptor-mediated endocytosis of virus by host cell / neutrophil chemotaxis / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / late endosome membrane / cell-cell junction / early endosome membrane / cytoplasmic vesicle / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / 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 / 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 / FYVE zinc finger ...PIKfyve, DEP domain / 1-phosphatidylinositol-3phosphate-5-kinase / 1-phosphatidylinositol-3-phosphate 5-kinase, PIPK catalytic domain / 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 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsLees JA / Reinisch KM
Funding support United States, 1 items
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, 2020-
Header (metadata) releaseOct 21, 2020-
Map releaseOct 21, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k2v
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7k2v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22647.png

Downloads & links

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Map

FileDownload / File: emd_22647.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPIKfyve/Fig4/Vac14 complex centered on PIKfyve - map2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.021901362 - 0.03785401
Average (Standard dev.)-0.000121809404 (±0.0006851084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0220.038-0.000

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Supplemental data

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Sample components

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Entire : PIKfyve/Fig4/Vac14 complex

EntireName: PIKfyve/Fig4/Vac14 complex
Components
  • Complex: PIKfyve/Fig4/Vac14 complex
    • Protein or peptide: 1-phosphatidylinositol 3-phosphate 5-kinase
    • Protein or peptide: 1-phosphatidylinositol 3-phosphate 5-kinase

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Supramolecule #1: PIKfyve/Fig4/Vac14 complex

SupramoleculeName: PIKfyve/Fig4/Vac14 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.28 MDa

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Macromolecule #1: 1-phosphatidylinositol 3-phosphate 5-kinase

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.462967 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: 1-phosphatidylinositol 3-phosphate 5-kinase

MacromoleculeName: 1-phosphatidylinositol 3-phosphate 5-kinase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.413039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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: Phosphoinositide kinase, FYVE-type zinc finger containing

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 58.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19998
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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