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- PDB-7bl1: human complex II-BATS bound to membrane-attached Rab5a-GTP -

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Basic information

Entry
Database: PDB / ID: 7bl1
Titlehuman complex II-BATS bound to membrane-attached Rab5a-GTP
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 gene protein
  • unknown peptide
KeywordsENDOCYTOSIS / Rab GTPase / Phosphatidylinositol 3-kinase
Function / homology
Function and homology information


regulation of protein serine/threonine kinase activity / lytic vacuole / maintenance of Golgi location / regulation of endosome size / nucleus-vacuole junction / cellular response to aluminum ion / cytoplasmic side of early endosome membrane / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade ...regulation of protein serine/threonine kinase activity / lytic vacuole / maintenance of Golgi location / regulation of endosome size / nucleus-vacuole junction / cellular response to aluminum ion / cytoplasmic side of early endosome membrane / positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / Synthesis of PIPs at the late endosome membrane / positive regulation of stress granule assembly / 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 / synaptic vesicle recycling / host-mediated activation of viral genome replication / amyloid-beta clearance by transcytosis / response to mitochondrial depolarisation / SARS-CoV-2 modulates autophagy / presynaptic endosome / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization / engulfment of apoptotic cell / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol kinase activity / host-mediated perturbation of viral process / positive regulation of autophagosome assembly / regulation of filopodium assembly / response to L-leucine / early endosome to late endosome transport / cytoplasmic side of mitochondrial outer membrane / negative regulation of autophagosome assembly / protein localization to phagophore assembly site / multivesicular body sorting pathway / receptor catabolic process / protein targeting to vacuole / SMAD protein signal transduction / RAB geranylgeranylation / protein targeting to lysosome / late endosome to vacuole transport / regulation of autophagosome assembly / endosome organization / pexophagy / RAB GEFs exchange GTP for GDP on RABs / early phagosome / double-strand break repair via classical nonhomologous end joining / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / positive regulation of autophagosome maturation / phosphatidylinositol-3-phosphate biosynthetic process / TBC/RABGAPs / cellular response to nitrogen starvation / centrosome cycle / negative regulation of programmed cell death / phosphatidylinositol 3-kinase / spindle organization / lysosome organization / 1-phosphatidylinositol-3-kinase activity / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / response to vitamin E / Macroautophagy / phosphatidylinositol-mediated signaling / response to iron(II) ion / positive regulation of cardiac muscle hypertrophy / SNARE complex assembly / p38MAPK cascade / RSV-host interactions / phosphatidylinositol phosphate biosynthetic process / regulation of synaptic vesicle exocytosis / Synthesis of PIPs at the plasma membrane / autolysosome / Respiratory syncytial virus (RSV) attachment and entry / autophagosome membrane / PI3K Cascade / positive regulation of exocytosis / axoneme / chromosome, centromeric region / autophagosome assembly / endocytic vesicle / amyloid-beta metabolic process / autophagosome maturation / RHO GTPases Activate NADPH Oxidases / synaptic vesicle endocytosis / regulation of macroautophagy / canonical Wnt signaling pathway / phagocytosis / neuron development / cellular defense response / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / intercellular bridge / positive regulation of intrinsic apoptotic signaling pathway / phagocytic vesicle / ruffle
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 / : / VPS15-like, helical domain / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain ...UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Serine/threonine-protein kinase Vps15-like / : / VPS15-like, helical domain / 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 / 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 / Trp-Asp (WD) repeats signature. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Protein kinase domain / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / 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'-TRIPHOSPHATE / Ras-related protein Rab-5A / Beclin-1 / Phosphatidylinositol 3-kinase catalytic subunit type 3 / Phosphoinositide 3-kinase regulatory subunit 4 / UV radiation resistance-associated gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.8 Å
AuthorsTremel, S. / Morado, D.R. / Kovtun, O. / Williams, R.L. / Briggs, J.A.G. / Munro, S. / Ohashi, Y. / Bertram, J. / Perisic, O.
Funding support United Kingdom, 7items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184308 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U10517878 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
Cancer Research UKC14801/A21211
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSION United Kingdom
Wellcome TrustNo. 103139 United Kingdom
Wellcome TrustNo. 203149 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes.
Authors: Shirley Tremel / Yohei Ohashi / Dustin R Morado / Jessie Bertram / Olga Perisic / Laura T L Brandt / Marie-Kristin von Wrisberg / Zhuo A Chen / Sarah L Maslen / Oleksiy Kovtun / Mark Skehel ...Authors: Shirley Tremel / Yohei Ohashi / Dustin R Morado / Jessie Bertram / Olga Perisic / Laura T L Brandt / Marie-Kristin von Wrisberg / Zhuo A Chen / Sarah L Maslen / Oleksiy Kovtun / Mark Skehel / Juri Rappsilber / Kathrin Lang / Sean Munro / John A G Briggs / Roger L Williams /
Abstract: The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal ...The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is generated by two complexes that both contain the lipid kinase VPS34: complex II on endosomes (VPS34/VPS15/Beclin 1/UVRAG), and complex I on autophagosomes (VPS34/VPS15/Beclin 1/ATG14L). The endosomal GTPase Rab5 binds complex II, but the mechanism of VPS34 activation by Rab5 has remained elusive, and no GTPase is known to bind complex I. Here we show that Rab5a-GTP recruits endocytic complex II to membranes and activates it by binding between the VPS34 C2 and VPS15 WD40 domains. Electron cryotomography of complex II on Rab5a-decorated vesicles shows that the VPS34 kinase domain is released from inhibition by VPS15 and hovers over the lipid bilayer, poised for catalysis. We also show that the GTPase Rab1a, which is known to be involved in autophagy, recruits and activates the autophagy-specific complex I, but not complex II. Both Rabs bind to the same VPS34 interface but in a manner unique for each. These findings reveal how VPS34 complexes are activated on membranes by specific Rab GTPases and how they are recruited to unique cellular locations.
History
DepositionJan 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
AAA: UV radiation resistance-associated gene protein
BBB: Phosphatidylinositol 3-kinase catalytic subunit type 3
CCC: Phosphoinositide 3-kinase regulatory subunit 4
EEE: Beclin-1
FFF: unknown peptide
DDD: Ras-related protein Rab-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,5818
Polymers407,0346
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 5 molecules AAABBBCCCEEEDDD

#1: Protein UV radiation resistance-associated gene protein / p63


Mass: 78258.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UVRAG / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9P2Y5
#2: 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
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
#3: Protein Phosphoinositide 3-kinase regulatory subunit 4 / PI3-kinase regulatory subunit 4 / PI3-kinase p150 subunit / Phosphoinositide 3-kinase adaptor protein


Mass: 154790.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
#4: 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
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197 / Cell line (production host): expi293F / Production host: Homo sapiens (human) / References: UniProt: Q14457
#6: Protein Ras-related protein Rab-5A


Mass: 18769.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5A, RAB5
Production host: Escherichia coli str. K-12 substr. DH10B (bacteria)
References: UniProt: P20339, small monomeric GTPase

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Protein/peptide , 1 types, 1 molecules FFF

#5: Protein/peptide unknown peptide


Mass: 1581.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293F / Production host: Homo sapiens (human)

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Non-polymers , 2 types, 2 molecules

#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5aCOMPLEXThe subunits were expressed using transient transfection in HEK293T cells. Cells were transfected with three plasmids: pYO1025 (encoding VPS34 and VPS15 in a pCAG backbone), pYO1124 (encoding UVGRAG 1-464 fused to the BATS of ATG14, residues 413-492 in pVAG) and pYO1006 (Beclin1 in pCAG)#1-#60MULTIPLE SOURCES
2human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG)COMPLEX#1-#51RECOMBINANT
3Ras-related protein Rab-5ACOMPLEX#61RECOMBINANT
Molecular weightValue: 392615 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Escherichia coli str. K-12 substr. DH10B (bacteria)316385
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESHEPES1
2200 mMNaClNaCl1
30.5 mMTCEPTCEP1
SpecimenConc.: 6.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quorum SC7620 / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 316 K / Details: Blot force 20, blot time 6 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.55 sec. / Electron dose: 2.99 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1
Image scansWidth: 6000 / Height: 4000

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Processing

SoftwareName: REFMAC / Version: 5.8.0272 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1MATLABR2016bvolume selectionThe locally written subTOM
2SerialEM3.8image acquisition
4NOVACTF1.0.0CTF correction
7Coot0.9model fittingFit as rigid bodies initially and the fit manually with coot
8ISOLDE1.1model fittingMD Flexible fit
11MATLABR2016bfinal Euler assignmentlocally written subTOM
12MATLABR2016bclassificationlocally written subTOM
13RELION3.13D reconstruction
14REFMAC5.8.0272model refinementused external restraints where high-resolution homologues were available
15ISOLDE1.1model refinementMD Flexible fit
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26979 / Algorithm: FOURIER SPACE / Symmetry type: POINT
EM volume selectionNum. of tomograms: 105 / Num. of volumes extracted: 191196 / Reference model: two Gaussian filtered elipsoids
Atomic model buildingB value: 320 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation
Details: An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. The model was refined in REFMAC with ...Details: An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. The model was refined in REFMAC with self-restraints (4.3) and restraints to 3MJH, 4DDP and 3IHY.
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
15DFZ

5dfz

5DFZ1
23MJH

3mjh

A3MJH2
34DDP

4ddp

A4DDP3
43IHY

3ihy

A3IHY4
RefinementResolution: 9.8→234.63 Å / Cor.coef. Fo:Fc: 0.954 / WRfactor Rwork: 0.1573 / SU B: 303.369 / SU ML: 1.88 / Average fsc overall: 0.9814 / Average fsc work: 0.9814
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rwork0.1573 11064 -
all0.1573 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 320.935 Å2
Baniso -1Baniso -2Baniso -3
1--6.184 Å21.147 Å2-0.935 Å2
2---1.872 Å25.156 Å2
3---8.056 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01115196
ELECTRON MICROSCOPYr_ext_dist_refined_d0.0030.1191935
ELECTRON MICROSCOPYr_angle_refined_deg1.9771.63321206
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.05952881
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.7423.67668
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.61815241
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.49156
ELECTRON MICROSCOPYr_chiral_restr0.1260.22778
ELECTRON MICROSCOPYr_gen_planes_refined0.010.0212322
ELECTRON MICROSCOPYr_nbd_refined0.2360.212534
ELECTRON MICROSCOPYr_nbtor_refined0.2660.221122
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.0810.2742
ELECTRON MICROSCOPYr_mcbond_it78.10149.72911560
ELECTRON MICROSCOPYr_mcangle_it136.30374.15814429
ELECTRON MICROSCOPYr_scbond_it86.10148.8663636
ELECTRON MICROSCOPYr_scangle_it135.45173.0926777
ELECTRON MICROSCOPYr_lrange_it264.0321652.509192054
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
9.8-10.0540.1568170.1568170.9890.156
10.054-10.3290.127890.127890.9920.12
10.329-10.6280.0957610.0957610.9930.095
10.628-10.9540.0717970.0717970.9940.071
10.954-11.3130.0676910.0676910.9940.067
11.313-11.7090.0717140.0717140.9940.071
11.709-12.150.0786630.0786630.9940.078
12.15-12.6440.0876860.0876860.9930.087
12.644-13.2050.1016270.1016270.9910.101
13.205-13.8470.1175990.1175990.9880.117
13.847-14.5930.1355840.1355840.9840.135
14.593-15.4750.1435230.1435230.9830.143
15.475-16.5380.1645240.1645240.9770.164
16.538-17.8560.1724710.1724710.9710.172
17.856-19.5490.24230.24230.9590.2
19.549-21.8370.2023820.2023820.9530.202
21.837-25.1790.243560.243560.9340.24
25.179-30.750.283040.283040.9090.28
30.75-43.1180.3072260.3072260.9310.307
43.118-234.630.3551270.3551270.9690.355

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