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- EMDB-56456: Cryo-EM structure of human VPS34-CI with ADP:MgF3 - local refinem... -

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Basic information

Entry
Database: EMDB / ID: EMD-56456
TitleCryo-EM structure of human VPS34-CI with ADP:MgF3 - local refinement on VPS34 and VPS15 kinases
Map data
Sample
  • Complex: Protein complex VPS34-CI with NRBF2 MIT and ADP:MgF3
    • Complex: Human VPS34-CI
    • Complex: NRBF2 MIT domain
KeywordsLipid kinase / Complex / Autophagy / LIPID BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsDessus AN / Williams RL
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184308 United Kingdom
Cancer Research UKDRCPGM 100014 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of human VPS34-CI with ADP:MgF3
Authors: Dessus AN / Williams RL
History
DepositionJan 22, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56456.png

Downloads & links

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Map

FileDownload / File: emd_56456.map.gz / Format: CCP4 / Size: 352.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 452 pix.
= 327.7 Å		0.73 Å/pix.
x 452 pix.
= 327.7 Å		0.73 Å/pix.
x 452 pix.
= 327.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0755
Minimum - Maximum-0.39899093 - 0.6419037
Average (Standard dev.)0.00042846316 (±0.013663192)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions452452452
Spacing452452452
CellA=B=C: 327.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56456_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56456_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Protein complex VPS34-CI with NRBF2 MIT and ADP:MgF3

EntireName: Protein complex VPS34-CI with NRBF2 MIT and ADP:MgF3
Components
  • Complex: Protein complex VPS34-CI with NRBF2 MIT and ADP:MgF3
    • Complex: Human VPS34-CI
    • Complex: NRBF2 MIT domain

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Supramolecule #1: Protein complex VPS34-CI with NRBF2 MIT and ADP:MgF3

SupramoleculeName: Protein complex VPS34-CI with NRBF2 MIT and ADP:MgF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140.86 KDa

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Supramolecule #2: Human VPS34-CI

SupramoleculeName: Human VPS34-CI / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: NRBF2 MIT domain

SupramoleculeName: NRBF2 MIT domain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
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

Concentration1.35 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMHEPESHEPES
100.0 mMNaClsodium chloride
1.0 mMTCEPTris-(2-Carboxyethyl)phosphine
4.0 mMCHAPSOCHAPSO
0.005 % (v/v)Nonidet-P-40Nonidet P-40
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 287.15 K / Instrument: FEI VITROBOT MARK II
Details3.6 uM VPS34-CI was mixed with 3.6 uM NRBF2 MIT, in presence of 13 mM MgCl2, 22.5 mM NaF and 2.5 mM ADP.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 8483 / Average exposure time: 1.66 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 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: 105000
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 #1

Image processing ID1
Particle selectionNumber selected: 306134
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

56346

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 55269
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 classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
Particle selectionNumber selected: 306134
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

56346

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 55269
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 classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9tw2


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: GABARAP chain F was removed
RefinementSpace: REAL

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