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Open data
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Basic information
Entry | Database: PDB / ID: 7bl1 | ||||||||||||||||||||||||
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Title | human complex II-BATS bound to membrane-attached Rab5a-GTP | ||||||||||||||||||||||||
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![]() | ENDOCYTOSIS / Rab GTPase / Phosphatidylinositol 3-kinase | ||||||||||||||||||||||||
Function / homology | ![]() lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / regulation of endosome size / nucleus-vacuole junction / postsynaptic early endosome / cellular response to aluminum ion / cytoplasmic side of early endosome membrane / Toll Like Receptor 9 (TLR9) Cascade / protein lipidation ...lytic vacuole / maintenance of Golgi location / regulation of protein serine/threonine kinase activity / regulation of endosome size / nucleus-vacuole junction / postsynaptic early endosome / 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 / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / synaptic vesicle recycling / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / amyloid-beta clearance by transcytosis / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation by host of viral genome replication / modulation by host of viral process / Synthesis of PIPs at the Golgi membrane / regulation of autophagosome assembly / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / engulfment of apoptotic cell / phosphatidylinositol kinase activity / protein localization to phagophore assembly site / suppression by virus of host autophagy / regulation of filopodium assembly / multivesicular body sorting pathway / RAB geranylgeranylation / protein targeting to lysosome / protein targeting to vacuole / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / SMAD protein signal transduction / double-strand break repair via classical nonhomologous end joining / RAB GEFs exchange GTP for GDP on RABs / early phagosome / Respiratory syncytial virus (RSV) attachment and entry / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / negative regulation of programmed cell death / response to iron(II) ion / TBC/RABGAPs / positive regulation of autophagosome maturation / centrosome cycle / SNARE complex assembly / autolysosome / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / spindle organization / mitotic metaphase chromosome alignment / regulation of synaptic vesicle exocytosis / Macroautophagy / cytoplasmic pattern recognition receptor signaling pathway / 1-phosphatidylinositol-3-kinase activity / lysosome organization / RSV-host interactions / positive regulation of cardiac muscle hypertrophy / positive regulation of exocytosis / p38MAPK cascade / axoneme / Synthesis of PIPs at the plasma membrane / autophagosome membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / mitophagy / autophagosome maturation / chromosome, centromeric region / autophagosome assembly / PI3K Cascade / RHO GTPases Activate NADPH Oxidases / response to vitamin E / autophagosome / neuron development / negative regulation of reactive oxygen species metabolic process / regulation of macroautophagy / canonical Wnt signaling pathway / amyloid-beta metabolic process / endomembrane system / cellular defense response / cellular response to glucose starvation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / phagocytosis / axon terminus / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / Prevention of phagosomal-lysosomal fusion / somatodendritic compartment / cellular response to epidermal growth factor stimulus Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.8 Å | ||||||||||||||||||||||||
![]() | Tremel, S. / Morado, D.R. / Kovtun, O. / Williams, R.L. / Briggs, J.A.G. / Munro, S. / Ohashi, Y. / Bertram, J. / Perisic, O. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 501.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 939.9 KB | Display | ![]() |
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Full document | ![]() | 946.7 KB | Display | |
Data in XML | ![]() | 67.7 KB | Display | |
Data in CIF | ![]() | 114.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12214MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() |
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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.) ![]() ![]() |
#3: Protein | Mass: 154790.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() 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.) ![]() ![]() |
#6: Protein | Mass: 18769.314 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() 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.) ![]() ![]() |
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-Non-polymers , 2 types, 2 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#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 |
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Sample preparation
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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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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 |
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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 | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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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: _ / Total num. of bins used: 20 / % reflection obs: 100 %
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