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- EMDB-41056: Local refinement map (1/2) of the human PI3KC3-C1 complex (EMD-40669) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-41056
TitleLocal refinement map (1/2) of the human PI3KC3-C1 complex (EMD-40669)
Map dataLocal refinement map (1/2) of the human PI3KC3-C1 complex (EMD-40669)
Sample
  • Complex: Human autophagy initiation PI3KC3-C1 complex
KeywordsAutophagy / Lipid kinase / Complex / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsChen M / Hurley JH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111730 United States
Michael J. Fox FoundationASAP-000350 United States
CitationJournal: bioRxiv / Year: 2023
Title: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex
Authors: Chen M / Ren X / Cook A / Hurley JH
History
DepositionJun 13, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJun 21, 2023-
Current statusJun 21, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41056.png

Downloads & links

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Map

FileDownload / File: emd_41056.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement map (1/2) of the human PI3KC3-C1 complex (EMD-40669)
Voxel sizeX=Y=Z: 1.115 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.1963131 - 2.337667
Average (Standard dev.)-0.0002075661 (±0.023898743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 401.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The according half map (1/2)

Fileemd_41056_half_map_1.map
AnnotationThe according half map (1/2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The according half map (2/2)

Fileemd_41056_half_map_2.map
AnnotationThe according half map (2/2)
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 autophagy initiation PI3KC3-C1 complex

EntireName: Human autophagy initiation PI3KC3-C1 complex
Components
  • Complex: Human autophagy initiation PI3KC3-C1 complex

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Supramolecule #1: Human autophagy initiation PI3KC3-C1 complex

SupramoleculeName: Human autophagy initiation PI3KC3-C1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 362 KDa

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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

Concentration0.25 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
300.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride
25.0 mMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Details: 25 mA
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) / Number grids imaged: 1 / Number real images: 2243 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1229932
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 226147
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 266147 / Software - Name: cryoSPARC (ver. 3.3.1)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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