+Open data
-Basic information
Entry | Database: PDB / ID: 7bl1 | ||||||||||||||||||||||||
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Title | human complex II-BATS bound to membrane-attached Rab5a-GTP | ||||||||||||||||||||||||
Components |
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Keywords | ENDOCYTOSIS / Rab GTPase / Phosphatidylinositol 3-kinase | ||||||||||||||||||||||||
Function / homology | Function and homology information lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / autophagy of peroxisome / regulation of endosome size / postsynaptic early endosome / nucleus-vacuole junction / cellular response to aluminum ion / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade ...lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / autophagy of peroxisome / regulation of endosome size / postsynaptic early endosome / nucleus-vacuole junction / cellular response to aluminum ion / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade / protein lipidation / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III / synaptic vesicle recycling / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation by host of viral genome replication / response to mitochondrial depolarisation / amyloid-beta clearance by transcytosis / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / modulation by host of viral process / Synthesis of PIPs at the Golgi membrane / positive regulation of autophagosome assembly / engulfment of apoptotic cell / regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / protein targeting to vacuole / protein targeting to lysosome / suppression by virus of host autophagy / regulation of filopodium assembly / RAB geranylgeranylation / multivesicular body sorting pathway / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / RAB GEFs exchange GTP for GDP on RABs / double-strand break repair via classical nonhomologous end joining / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / early phagosome / SMAD protein signal transduction / phosphatidylinositol-mediated signaling / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / response to iron(II) ion / negative regulation of programmed cell death / TBC/RABGAPs / centrosome cycle / SNARE complex assembly / positive regulation of autophagosome maturation / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / regulation of synaptic vesicle exocytosis / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / spindle organization / mitotic metaphase chromosome alignment / lysosome organization / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of exocytosis / p38MAPK cascade / axoneme / autophagosome maturation / autophagosome membrane / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / mitophagy / autophagosome assembly / chromosome, centromeric region / RHO GTPases Activate NADPH Oxidases / PI3K Cascade / neuron development / autophagosome / canonical Wnt signaling pathway / negative regulation of reactive oxygen species metabolic process / response to vitamin E / regulation of macroautophagy / endomembrane system / cellular response to glucose starvation / cellular defense response / phosphatidylinositol 3-kinase binding / phagocytic vesicle / amyloid-beta metabolic process / axon terminus / phagocytosis / positive regulation of autophagy / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / somatodendritic compartment / Prevention of phagosomal-lysosomal fusion / cellular response to epidermal growth factor stimulus / ruffle Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.8 Å | ||||||||||||||||||||||||
Authors | Tremel, 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
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7bl1.cif.gz | 496.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bl1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7bl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/7bl1 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/7bl1 | HTTPS FTP |
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-Related structure data
Related structure data | 12214MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 5 molecules AAABBBCCCEEEDDD
#1: Protein | 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 |
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#2: Protein | 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 | 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 | 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 | 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 |
-Protein/peptide , 1 types, 1 molecules FFF
#5: Protein/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 / |
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#8: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component |
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Molecular weight | Value: 392615 kDa/nm / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 6.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Details: Quorum SC7620 / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 316 K / Details: Blot force 20, blot time 6 s |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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 scans | Width: 6000 / Height: 4000 |
-Processing
Software | Name: REFMAC / Version: 5.8.0272 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26979 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 105 / Num. of volumes extracted: 191196 / Reference model: two Gaussian filtered elipsoids | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B 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 |
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Refinement | Resolution: 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
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Solvent computation | Solvent model: BABINET MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 320.935 Å2
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Refine LS restraints |
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LS refinement shell | Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: 0 / Total num. of bins used: 20 / % reflection obs: 100 %
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