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Yorodumi- PDB-9b8q: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9b8q | ||||||
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Title | Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks | ||||||
Components |
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Keywords | PROTON TRANSPORT / Complex / Synaptic / Native | ||||||
Function / homology | Function and homology information Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / intracellular organelle / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / clathrin-coated vesicle membrane ...Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / intracellular organelle / synaptic vesicle lumen acidification / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / transmembrane transporter complex / regulation of macroautophagy / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / terminal bouton / synaptic vesicle membrane / endocytosis / melanosome / synaptic vesicle / apical part of cell / ATPase binding / endosome / apical plasma membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Coupland, C.E. / Rubinstein, J.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Science / Year: 2024 Title: High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles. Authors: Claire E Coupland / Ryan Karimi / Stephanie A Bueler / Yingke Liang / Gautier M Courbon / Justin M Di Trani / Cassandra J Wong / Rayan Saghian / Ji-Young Youn / Lu-Yang Wang / John L Rubinstein / Abstract: Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or ...Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single-particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in a loss of the V region of V-ATPase from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9b8q.cif.gz | 321.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9b8q.ent.gz | 236.4 KB | Display | PDB format |
PDBx/mmJSON format | 9b8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b8q_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 9b8q_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 9b8q_validation.xml.gz | 58.3 KB | Display | |
Data in CIF | 9b8q_validation.cif.gz | 90.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/9b8q ftp://data.pdbj.org/pub/pdb/validation_reports/b8/9b8q | HTTPS FTP |
-Related structure data
Related structure data | 44352MC 9b8oC 9b8pC 9brbC 9brcC 9brdC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 43958.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5FVI6 | ||||||
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#2: Protein | Mass: 26167.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PCU2 #3: Protein | Mass: 13690.476 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q8R2H0 #4: Protein | | Mass: 55936.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A8I5ZQ24 #5: Protein | | Mass: 96429.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P25286 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, peripheral stalks Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 37.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21_5207 / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198533 / Symmetry type: POINT |