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- EMDB-76934: Cryo-EM reconstruction of human PI3KC3-C1, composite map -

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Basic information

Entry
Database: EMDB / ID: EMD-76934
TitleCryo-EM reconstruction of human PI3KC3-C1, composite map
Map dataComposite map
Sample
  • Complex: Human Phosphatidylinositol-3 kinase class III complex I
KeywordsLipid kinase / autophagosome formation / signaling protein / IMMUNE SYSTEM
Function / homology
Function and homology information


extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / extrinsic component of phagophore assembly site membrane / regulation of triglyceride metabolic process / nucleus-vacuole junction / cellular response to aluminum ion / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / positive regulation of stress granule assembly ...extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / extrinsic component of phagophore assembly site membrane / regulation of triglyceride metabolic process / nucleus-vacuole junction / cellular response to aluminum ion / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / positive regulation of stress granule assembly / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / mitochondria-associated endoplasmic reticulum membrane contact site / presynaptic endosome / positive regulation of attachment of mitotic spindle microtubules to kinetochore / host-mediated activation of viral genome replication / negative regulation of lysosome organization / engulfment of apoptotic cell / regulation of protein complex stability / phosphatidylinositol kinase activity / positive regulation of autophagosome assembly / phosphatidylinositol 3-kinase regulator activity / Synthesis of PIPs at the Golgi membrane / cytoplasmic side of mitochondrial outer membrane / early endosome to late endosome transport / negative regulation of autophagosome assembly / phagophore assembly site membrane / protein localization to phagophore assembly site / receptor catabolic process / response to L-leucine / protein targeting to vacuole / SMAD protein signal transduction / late endosome to vacuole transport / protein targeting to lysosome / endosome organization / pexophagy / positive regulation of natural killer cell mediated cytotoxicity / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / cellular response to nitrogen starvation / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / negative regulation of programmed cell death / 1-phosphatidylinositol-3-kinase activity / post-transcriptional regulation of gene expression / mitotic metaphase chromosome alignment / response to vitamin E / lysosome organization / Macroautophagy / endosome to lysosome transport / response to iron(II) ion / autophagosome membrane docking / positive regulation of cardiac muscle hypertrophy / RSV-host interactions / p38MAPK cascade / negative regulation of protein phosphorylation / cytoplasmic pattern recognition receptor signaling pathway / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / autolysosome / autophagosome membrane / PI3K Cascade / protein secretion / amyloid-beta metabolic process / RHO GTPases Activate NADPH Oxidases / regulation of macroautophagy / autophagosome maturation / axoneme / neuron development / synaptic vesicle endocytosis / cellular defense response / autophagosome assembly / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / intercellular bridge / JNK cascade / phagocytic vesicle / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / positive regulation of autophagy / autophagosome / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / cellular response to starvation / regulation of cytokinesis / regulation of autophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / trans-Golgi network / phosphatidylinositol 3-kinase/protein kinase B signal transduction / circadian rhythm / protein processing / positive regulation of protein phosphorylation
Similarity search - Function
UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain ...UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Phosphatidylinositol 3-kinase, Vps34 type / : / : / Phosphatase 2A Regulatory Subunit A, helical domain / HEAT repeat profile. / HEAT, type 2 / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats signature. / Protein kinase domain / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Serine/Threonine protein kinases, catalytic domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Beclin-1 / Beclin 1-associated autophagy-related key regulator / Phosphatidylinositol 3-kinase catalytic subunit type 3 / Phosphoinositide 3-kinase regulatory subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsChen M / Hurley JH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS134598 United States
Michael J. Fox FoundationASAP-000350 United States
CitationJournal: To Be Published
Title: Cryo-EM reconstruction of PI3KC3-C2 in complex with Rubicon Middle Region of C terminus
Authors: Chen M / Hurley JH
History
DepositionApr 27, 2026-
SupersessionMay 13, 2026ID: EMD-40669
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76934.png

Downloads & links

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Map

FileDownload / File: emd_76934.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 400 pix.
= 446. Å		1.12 Å/pix.
x 400 pix.
= 446. Å		1.12 Å/pix.
x 400 pix.
= 446. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.115 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.16679692 - 1.3267035
Average (Standard dev.)0.003643455 (±0.015242554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 446.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human Phosphatidylinositol-3 kinase class III complex I

EntireName: Human Phosphatidylinositol-3 kinase class III complex I
Components
  • Complex: Human Phosphatidylinositol-3 kinase class III complex I

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Supramolecule #1: Human Phosphatidylinositol-3 kinase class III complex I

SupramoleculeName: Human Phosphatidylinositol-3 kinase class III complex I
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

Concentration0.45 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
200.0 mMNaClSodium chloride
2.0 mMMgCl2Magnesium chloride
25.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
1.0 mMTCEPTris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9mhf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2)
Details: Composed from two local refinement maps, of which resolutions are 3.29 and 3.26 A, respectively
Number images used: 181267
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.6.2)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: 9MHF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 82.1
Output model

PDB-13bv:
Cryo-EM structure of human PI3KC3-C1 complex

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