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- EMDB-48273: PI3KC3-C1 bound to RAB1A, VPS34 in active state. -

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Basic information

Entry
Database: EMDB / ID: EMD-48273
TitlePI3KC3-C1 bound to RAB1A, VPS34 in active state.
Map data
Sample
  • Complex: Phosphatidylinositol-3 kinase class III complex I bound to RAB1A
KeywordsComplex / GTPase / GTP-binding / Autophagy / Kinase / Lipid Kinase / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsCook ASI / Chen M / Hurley JH
Funding support United States, 1 items
OrganizationGrant numberCountry
Aligning Science Across Parkinsons (ASAP)ASAP-000350 United States
CitationJournal: To Be Published
Title: Structural pathway for class III PI 3-kinase activation by the myristoylated GTPbinding pseudokinase VPS15
Authors: Cook ASI / Chen M / Ngyuen TN / Claveras-Cabezudo A / Khuu G / Rao S / Garcia SN / Yang M / Iavarone AT / Ren X / Lazarou M / Hummer G / Hurley JH
History
DepositionDec 11, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48273.png

Downloads & links

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Map

FileDownload / File: emd_48273.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 419.2 Å		1.05 Å/pix.
x 400 pix.
= 419.2 Å		1.05 Å/pix.
x 400 pix.
= 419.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.83266205 - 1.1138983
Average (Standard dev.)-0.00032930286 (±0.016733246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48273_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_48273_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48273_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Phosphatidylinositol-3 kinase class III complex I bound to RAB1A

EntireName: Phosphatidylinositol-3 kinase class III complex I bound to RAB1A
Components
  • Complex: Phosphatidylinositol-3 kinase class III complex I bound to RAB1A

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Supramolecule #1: Phosphatidylinositol-3 kinase class III complex I bound to RAB1A

SupramoleculeName: Phosphatidylinositol-3 kinase class III complex I bound to RAB1A
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 384.45 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

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
2.0 mMMgCl2Magnesium chloride
1.0 mMC9H15O6PTCEP

Details: OG supplemented at time of grid preparation 0.05%
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsmonodisperse sample

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 19300 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8sor


Details: Made in silico, low pass map to start classifying PI3KC3-C1 shaped particles.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 151763
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: 3 / Software - Name: cryoSPARC (ver. 3.3.1)
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

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