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- EMDB-22631: PIKfyve/Fig4/Vac14 complex centered on Fig4 - map3 -

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Basic information

Entry
Database: EMDB / ID: EMD-22631
TitlePIKfyve/Fig4/Vac14 complex centered on Fig4 - map3
Map dataPIKfyve complex density map centered on Fig4
Sample
  • Complex: PIKfyve/Fig4/Vac14 complex
    • Protein or peptide: Fig4 Sac homology model
KeywordsLipid kinase / Lipid phosphatase / protein complex / LIPID BINDING PROTEIN
Function / homology
Function and homology information


phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / myelin assembly / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / negative regulation of myelination / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ...phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity / myelin assembly / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / negative regulation of myelination / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase / phosphoinositide 5-phosphatase / phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / vacuole organization / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatidylinositol biosynthetic process / pigmentation / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / neuron development / lipid droplet / locomotory behavior / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 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 8, 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: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k1w
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7k1w
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22631.png

Downloads & links

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Map

FileDownload / File: emd_22631.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPIKfyve complex density map centered on Fig4
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: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.022210082 - 0.046168517
Average (Standard dev.)-0.00006561446 (±0.0013303686)
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-0.0220.046-0.000

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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: Fig4 Sac homology model

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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: Fig4 Sac homology model

MacromoleculeName: Fig4 Sac homology model / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.144289 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHG SMPTAAAPII SSVQKLVLYE TRARYFLVGS NNAETKYRVL KIDRTEPKDL VIIDDRHVYT QQEVRELLGR LDLGNRTKM GQKGSSGLFR AVSAFGVVGF VRFLEGYYIV LITKRRKMAD IGGHAIYKVE DTNMIYIPND SVRVTHPDEA R YLRIFQNV ...String:
MHHHHHHHHG SMPTAAAPII SSVQKLVLYE TRARYFLVGS NNAETKYRVL KIDRTEPKDL VIIDDRHVYT QQEVRELLGR LDLGNRTKM GQKGSSGLFR AVSAFGVVGF VRFLEGYYIV LITKRRKMAD IGGHAIYKVE DTNMIYIPND SVRVTHPDEA R YLRIFQNV DLSSNFYFSY SYDLSHSLQY NLTVLRMPLE MLKSEMTQNR QESFDIFEDE GLITQGGSGV FGICSEPYMK YV WNGELLD IIKSTVHRDW LLYIIHGFCG QSKLLIYGRP VYVTLIARRS SKFAGTRFLK RGANCEGDVA NEVETEQILC DAS VMSFTA GSYSSYVQVR GSVPLYWSQD ISTMMPKPPI TLDQADPFAH VAALHFDQMF QRFGSPIIIL NLVKEREKRK HERI LSEEL VAAVTYLNQF LPPEHTIVYI PWDMAKYTKS KLCNVLDRLN VIAESVVKKT GFFVNRPDSY CSILRPDEKW NELGG CVIP TGRLQTGILR TNCVDCLDRT NTAQFMVGKC ALAYQLYSLG LIDKPNLQFD TDAVRLFEEL YEDHGDTLSL QYGGSQ LVH RVKTYRKIAP WTQHSKDIMQ TLSRYYSNAF SDADRQDSIN LFLGVFHPTE GKPHLWELPT DFYLHHKNTM RLLPTRR SY TYWWTPEVIK HLPLPYDEVI CAVNLKKLIV KKFHKYEEEI DIHNEFFRPY ELSSFDDTFC LAMTSSARDF MPKTVGID P SPFTVRKPDE TGKSVLGNKS NREEAVLQRK TAASAPPPPS EEAVSSSSED DSGTDREEEG SVSQRSTPVK MTDAGDSAK VTENVVQPMK ELYGINLSDG LSEEDFSIYS RFVQLGQSQH KQDKNSQQPC SRCSDGVIKL TPISAFSQDN IYEVQPPRVD RKSTEIFQA HIQASQGIMQ PLGKEDSSMY REYIRNRYL

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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: 5.1 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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