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- PDB-9rxa: VPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS1... -

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Basic information

Entry
Database: PDB / ID: 9rxa
TitleVPS34-CII bound to RAB5A-GTP 1-212 (C19S, C63S, Q79L) on the VPS15 subunit
Components
  • Beclin-1
  • Phosphatidylinositol 3-kinase catalytic subunit type 3
  • Phosphoinositide 3-kinase regulatory subunit 4
  • Ras-related protein Rab-5A
  • UV radiation resistance associated protein
KeywordsENDOCYTOSIS / Lipid kinase / GTPase / kinase / endocytic trafficking / endosome maturation / SIGNALING PROTEIN
Function / homology
Function and homology information


protein-containing complex organization / regulation of endosome size / nucleus-vacuole junction / cytoplasmic side of early endosome membrane / cellular response to aluminum ion / protein localization to early endosome / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / positive regulation of stress granule assembly ...protein-containing complex organization / regulation of endosome size / nucleus-vacuole junction / cytoplasmic side of early endosome membrane / cellular response to aluminum ion / protein localization to early endosome / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / positive regulation of stress granule assembly / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / amyloid-beta clearance by transcytosis / response to mitochondrial depolarisation / synaptic vesicle recycling / presynaptic endosome / positive regulation of attachment of mitotic spindle microtubules to kinetochore / host-mediated activation of viral genome replication / plasma membrane to endosome transport / negative regulation of lysosome organization / engulfment of apoptotic cell / host-mediated perturbation of viral process / phosphatidylinositol kinase activity / positive regulation of autophagosome assembly / regulation of filopodium assembly / Synthesis of PIPs at the Golgi membrane / cytoplasmic side of mitochondrial outer membrane / early endosome to late endosome transport / negative regulation of autophagosome assembly / protein localization to phagophore assembly site / receptor catabolic process / RAB geranylgeranylation / response to L-leucine / protein targeting to vacuole / SMAD protein signal transduction / late endosome to vacuole transport / protein targeting to lysosome / regulation of autophagosome assembly / endosome organization / pexophagy / RAB GEFs exchange GTP for GDP on RABs / early phagosome / positive regulation of natural killer cell mediated cytotoxicity / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / TBC/RABGAPs / cellular response to nitrogen starvation / centrosome cycle / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / negative regulation of programmed cell death / endosomal transport / 1-phosphatidylinositol-3-kinase activity / mitotic metaphase chromosome alignment / response to vitamin E / lysosome organization / Macroautophagy / response to iron(II) ion / positive regulation of cardiac muscle hypertrophy / RSV-host interactions / regulation of synaptic vesicle exocytosis / p38MAPK cascade / cytoplasmic pattern recognition receptor signaling pathway / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / Synthesis of PIPs at the plasma membrane / autolysosome / positive regulation of exocytosis / Respiratory syncytial virus (RSV) attachment and entry / PI3K Cascade / protein secretion / amyloid-beta metabolic process / chromosome, centromeric region / RHO GTPases Activate NADPH Oxidases / regulation of macroautophagy / autophagosome maturation / endocytic vesicle / canonical Wnt signaling pathway / axoneme / neuron development / synaptic vesicle endocytosis / cellular defense response / phagocytosis / autophagosome assembly / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / intercellular bridge / JNK cascade / phagocytic vesicle / ruffle / positive regulation of intrinsic apoptotic signaling pathway / vesicle-mediated transport / somatodendritic compartment / endomembrane system / Prevention of phagosomal-lysosomal fusion
Similarity search - Function
UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain ...UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Phosphatidylinositol 3-kinase, Vps34 type / : / : / Phosphatase 2A Regulatory Subunit A, helical domain / HEAT repeat profile. / HEAT, type 2 / Small GTPase Rab domain profile. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / WD domain, G-beta repeat / Armadillo-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats signature. / Protein kinase domain / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Serine/Threonine protein kinases, catalytic domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / MYRISTIC ACID / Ras-related protein Rab-5A / Beclin-1 / UV radiation resistance associated protein / Phosphatidylinositol 3-kinase catalytic subunit type 3 / Phosphoinositide 3-kinase regulatory subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsSpokaite, S. / Ohashi, Y. / Dessus, A.N. / Bourguet, M. / Williams, R.L.
Funding support United Kingdom, 2items
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, A.N. / Williams, R.L.
History
DepositionJul 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 3-kinase catalytic subunit type 3
B: Phosphoinositide 3-kinase regulatory subunit 4
C: Beclin-1
D: UV radiation resistance associated protein
F: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,22411
Polymers409,9165
Non-polymers1,3096
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 5 molecules ABCDF

#1: Protein Phosphatidylinositol 3-kinase catalytic subunit type 3 / PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase ...PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase class 3 / hVps34


Mass: 101680.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full length untagged VPS34 / Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3, VPS34 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q8NEB9, phosphatidylinositol 3-kinase
#2: Protein Phosphoinositide 3-kinase regulatory subunit 4 / PI3-kinase regulatory subunit 4 / PI3-kinase p150 subunit / Phosphoinositide 3-kinase adaptor protein


Mass: 154659.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full length VPS15 with 13 extra residues at the C-terminal left after TEV cleavage (VPS15-SRPTTASENLYFQ)
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R4, VPS15 / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
References: UniProt: Q99570, non-specific serine/threonine protein kinase
#3: Protein Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 51953.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Full length BECLIN1 / Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q14457
#4: Protein UV radiation resistance associated protein


Mass: 78289.852 Da / Num. of mol.: 1 / Mutation: P10Q
Source method: isolated from a genetically manipulated source
Details: Full length UVRAG with a P10Q mutation / Source: (gene. exp.) Homo sapiens (human) / Gene: UVRAG / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q6P1X0
#5: Protein Ras-related protein Rab-5A


Mass: 23333.225 Da / Num. of mol.: 1 / Mutation: C19S, C63S, Q79L
Source method: isolated from a genetically manipulated source
Details: RAB5A 1-212 loaded with GTP, with C19S, C63S, Q79L mutations
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5A, RAB5 / Production host: Escherichia coli (E. coli) / Strain (production host): OverExpress(TM) C41(DE3) / References: UniProt: P20339, small monomeric GTPase

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Non-polymers , 5 types, 6 molecules

#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human VPS34-CII (VPS34/VPS15/BECLIN1/UVRAG) incubated with 22-fold molar excess of RAB5A-GTP (C19S, C63S, Q79L)
Type: COMPLEX / Details: RAB5A is bound to the VPS15 subunit in this class / Entity ID: #5, #1, #4, #3 / Source: RECOMBINANT
Molecular weightValue: 0.432 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2200 mMSodium chlorideNaCl1
31 mMTCEPC9H15O6P1
45 mMMagnesium chlorideMgCl21
51 mMAMPPNPC10H17N6O12P31
64 mMCHAPSOC32H58N2O8S1
70.005 % v/vNonidet P40 substitute(C2H4O)nC14H22O1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was crosslinked with 20 uM BS3 for 20 minutes on ice, then quenched with 100 mM TRIS pH 8.0 prior to vitrification
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 287 K
Details: 3.5 uL sample, 0 second wait, 4 second blot, blot force +8

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 19844
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1crYOLO1.7.5particle selection
2PHENIX1.21rc1_5156:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 717560
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70445 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00324557
ELECTRON MICROSCOPYf_angle_d0.68833204
ELECTRON MICROSCOPYf_dihedral_angle_d8.0843273
ELECTRON MICROSCOPYf_chiral_restr0.0453687
ELECTRON MICROSCOPYf_plane_restr0.0064262

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