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Open data
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Basic information
Entry | Database: PDB / ID: 9brd | ||||||
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Title | Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 | ||||||
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![]() | PROTON TRANSPORT / Vesicle / synaptic / membrane | ||||||
Function / homology | ![]() regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / RHOA GTPase cycle / Insulin receptor recycling / eye pigmentation / central nervous system maturation / transporter activator activity ...regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Transferrin endocytosis and recycling / Ion channel transport / Amino acids regulate mTORC1 / RHOA GTPase cycle / Insulin receptor recycling / eye pigmentation / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / positive regulation of transforming growth factor beta1 production / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / intracellular organelle / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / proton-transporting V-type ATPase complex / neuron spine / head morphogenesis / protein localization to cilium / regulation of short-term neuronal synaptic plasticity / neuron projection terminus / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / syntaxin-1 binding / vacuolar acidification / osteoclast development / ROS and RNS production in phagocytes / Neutrophil degranulation / regulation of synaptic vesicle exocytosis / : / ATPase complex / cholesterol binding / presynaptic active zone / regulation of neuronal synaptic plasticity / autophagosome membrane / response to amyloid-beta / microvillus / regulation of MAPK cascade / ATPase activator activity / synaptic vesicle endocytosis / excitatory synapse / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / regulation of macroautophagy / angiotensin maturation / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / RNA endonuclease activity / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / SH2 domain binding / proton-transporting ATP synthase activity, rotational mechanism / SNARE binding / receptor-mediated endocytosis / secretory granule / regulation of long-term neuronal synaptic plasticity / Schaffer collateral - CA1 synapse / neuromuscular junction / terminal bouton / transmembrane transport / synaptic vesicle membrane / small GTPase binding / cilium / endocytosis / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / presynapse / apical part of cell / presynaptic membrane / signaling receptor activity / cell body / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / lysosome / early endosome / endosome membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Coupland, C.E. / Rubinstein, J.L. | ||||||
Funding support | ![]()
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![]() | ![]() 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 loss of V 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.8 MB | Display | ![]() |
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Full document | ![]() | 3.9 MB | Display | |
Data in XML | ![]() | 228 KB | Display | |
Data in CIF | ![]() | 353.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 44353MC ![]() 9b8oC ![]() 9b8pC ![]() 9b8qC ![]() 9brbC ![]() 9brcC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 7 types, 11 molecules ABCHQRSUbfp
#1: Protein | Mass: 71368.352 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: D4A133, H+-transporting two-sector ATPase #4: Protein | | Mass: 28359.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 65505.297 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0968 / Production host: ![]() ![]() #11: Protein | | Mass: 33331.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | | Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | | Mass: 9502.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | | Mass: 39118.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-V-type proton ATPase ... , 11 types, 25 molecules DEFGIJKLMNOPTadeghijklmno
#2: Protein | Mass: 56611.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 43958.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 26167.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | | Mass: 13389.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 13690.476 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | | Mass: 51160.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | | Mass: 53695.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | | Mass: 95722.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | | Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | | Mass: 9203.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 3 types, 10 molecules ![](data/chem/img/NAG.gif)
#19: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #20: Polysaccharide | alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D- ...alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #25: Sugar | ChemComp-NAG / | |
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-Non-polymers , 6 types, 47 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/WJP.gif)
![](data/chem/img/LP3.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/PTY.gif)
![](data/chem/img/WJP.gif)
![](data/chem/img/LP3.gif)
![](data/chem/img/CLR.gif)
#21: Chemical | ChemComp-ADP / | ||||||||
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#22: Chemical | ChemComp-PC1 / #23: Chemical | ChemComp-PTY / #24: Chemical | ChemComp-WJP / | #26: Chemical | ChemComp-LP3 / ( | #27: Chemical | ChemComp-CLR / |
-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 |
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Sample preparation
Component | Name: V-type proton ATPase / Type: COMPLEX / Entity ID: #2-#11, #13-#15, #17-#18 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
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) |
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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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198766 / Symmetry type: POINT |