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Yorodumi- PDB-9b8p: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 9b8p | ||||||
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Title | Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 | ||||||
Components |
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Keywords | PROTON TRANSPORT / Mmebrane / Synaptic / Complex | ||||||
Function / homology | Function and homology information Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / Insulin receptor recycling / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / 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 / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / 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, V1 domain / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / protein localization to cilium / vacuolar acidification / regulation of cellular pH / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / cilium assembly / transmembrane transporter complex / H+-transporting two-sector ATPase / ATP metabolic process / ruffle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / secretory granule / cilium / synaptic vesicle membrane / melanosome / ATPase binding / intracellular iron ion homeostasis / endosome / apical plasma membrane / centrosome / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Coupland, E.M. / 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 | 9b8p.cif.gz | 966.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9b8p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9b8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b8p_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 9b8p_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 9b8p_validation.xml.gz | 129.5 KB | Display | |
Data in CIF | 9b8p_validation.cif.gz | 199.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/9b8p ftp://data.pdbj.org/pub/pdb/validation_reports/b8/9b8p | HTTPS FTP |
-Related structure data
Related structure data | 44351MC 9b8oC 9b8qC 9brbC 9brcC 9brdC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 7 molecules ABCHQRS
#1: Protein | Mass: 71483.438 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) References: UniProt: D4A133, H+-transporting two-sector ATPase #3: Protein | | Mass: 28359.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P503 #7: Protein | Mass: 65505.297 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Gene: lpg0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWW6 |
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-V-type proton ATPase subunit ... , 4 types, 10 molecules DEFIJKLMNO
#2: Protein | Mass: 56611.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62815 #4: 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 #5: Protein | | Mass: 13389.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P50408 #6: 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 |
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-Non-polymers , 1 types, 1 molecules
#8: Chemical | ChemComp-ADP / |
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-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: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES |
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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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198533 / Symmetry type: POINT |