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- EMDB-54313: VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RA... -

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Basic information

Entry
Database: EMDB / ID: EMD-54313
TitleVPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L, focused refinement on the kinase arm)
Map data
Sample
  • Complex: Human VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) in complex with RAB5A-GTP (C19S, C63S, Q70L)
KeywordsLipid kinase / GTPase / kinase / autophagy / endocytic trafficking / SIGNALING PROTEIN / ENDOCYTOSIS
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsSpokaite S / Ohashi Y / Bourguet M / Dessus 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: Elife / Year: 2026
Title: A novel RAB5 binding site in human VPS34-CII that is likely the primordial site in eukaryotic evolution
Authors: Spokaite S / Ohashi Y / Bourguet M / Dessus AN / Williams RL
History
DepositionJul 9, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54313.png

Downloads & links

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Map

FileDownload / File: emd_54313.map.gz / Format: CCP4 / Size: 259.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 408 pix.
= 350.88 Å		0.86 Å/pix.
x 408 pix.
= 350.88 Å		0.86 Å/pix.
x 408 pix.
= 350.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.2976087 - 1.1698515
Average (Standard dev.)0.0028590937 (±0.027591266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions408408408
Spacing408408408
CellA=B=C: 350.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54313_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54313_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54313_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) in complex with RAB5A...

EntireName: Human VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) in complex with RAB5A-GTP (C19S, C63S, Q70L)
Components
  • Complex: Human VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) in complex with RAB5A-GTP (C19S, C63S, Q70L)

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Supramolecule #1: Human VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) in complex with RAB5A...

SupramoleculeName: Human VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) in complex with RAB5A-GTP (C19S, C63S, Q70L)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Details: RAB5A bound to VPS15 is partially resolved
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 432 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

Concentration2.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
200.0 mMNaClSodium chloride
1.0 mMC9H15O6PTCEP
5.0 mMMgCl2Magnesium chloride
1.0 mMC10H17N6O12P3AMPPNP
4.0 mMC32H58N2O8SCHAPSO
0.005 % v/v(C2H4O)nC14H22ONonidet P40 substitute
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 287 K / Instrument: FEI VITROBOT MARK III
Details: 3.5 uL sample, 0 second wait, 4 second blot, blot force +8.
DetailsSample was crosslinked with 30 uM BS3 for 20 minutes on ice, then quenched with 100 mM TRIS pH 8.0 prior to vitrification

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10739 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 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

CTF correctionType: NONE
Startup modelType of model: OTHER
Details: Density from VPS34-CI bound to NRBF2 MIT domain, determined earlier
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 151160
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: UCSF ChimeraX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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