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- EMDB-74521: Cryo-EM reconstruction of PI3KC3-C2 in complex with Rubicon Middl... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-74521
TitleCryo-EM reconstruction of PI3KC3-C2 in complex with Rubicon Middle Region of C terminus, focused map 2/2
Map dataSharpened map
Sample
  • Complex: Human Phosphatidylinositol-3 kinase class III complex II in complex with Rubicon Middle Region of C terminus
KeywordsLipid kinase / endocytic sorting / cytokinesis / autophagosome maturation / lysosome recycling / LC3-associated phagocytosis / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsChen M / Ni Q / 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 / Ni Q / Hurley JH
History
DepositionDec 16, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74521.png

Downloads & links

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Map

FileDownload / File: emd_74521.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 448 pix.
= 421.12 Å		0.94 Å/pix.
x 448 pix.
= 421.12 Å		0.94 Å/pix.
x 448 pix.
= 421.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.5484357 - 2.011673
Average (Standard dev.)0.00017082498 (±0.02210532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 421.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_74521_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_74521_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Phosphatidylinositol-3 kinase class III complex II in compl...

EntireName: Human Phosphatidylinositol-3 kinase class III complex II in complex with Rubicon Middle Region of C terminus
Components
  • Complex: Human Phosphatidylinositol-3 kinase class III complex II in complex with Rubicon Middle Region of C terminus

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Supramolecule #1: Human Phosphatidylinositol-3 kinase class III complex II in compl...

SupramoleculeName: Human Phosphatidylinositol-3 kinase class III complex II in complex with Rubicon Middle Region of C terminus
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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
200.0 mMNaClSodium chloride
2.0 mMMgCl2Magnesium chloride
25.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
1.0 mMTris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 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: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold prediction model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 175726
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 95.23

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