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Yorodumi- PDB-9bry: V0-only V-ATPase in synaptophysin gene knock-out mouse brain isol... -
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-Basic information
Entry | Database: PDB / ID: 9bry | |||||||||
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Title | V0-only V-ATPase in synaptophysin gene knock-out mouse brain isolated synaptic vesicles | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / V0only V-ATPase / synaptic vesicle | |||||||||
Function / homology | Function and homology information Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / transporter activator activity / eye pigmentation / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex ...Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / transporter activator activity / eye pigmentation / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / rostrocaudal neural tube patterning / RHOA GTPase cycle / positive regulation of transforming growth factor beta1 production / cellular response to increased oxygen levels / intracellular organelle / ROS and RNS production in phagocytes / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / P-type proton-exporting transporter activity / lysosomal lumen acidification / clathrin-coated vesicle membrane / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar transport / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar proton-transporting V-type ATPase complex / osteoclast development / vacuolar acidification / dendritic spine membrane / regulation of cellular pH / regulation of MAPK cascade / ATPase activator activity / autophagosome membrane / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / endomembrane system / regulation of macroautophagy / angiotensin maturation / axon terminus / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / Neutrophil degranulation / receptor-mediated endocytosis / proton transmembrane transport / transmembrane transport / small GTPase binding / synaptic vesicle membrane / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / signaling receptor activity / ATPase binding / cell body / postsynaptic membrane / intracellular iron ion homeostasis / Hydrolases; Acting on ester bonds / receptor-mediated endocytosis of virus by host cell / positive regulation of ERK1 and ERK2 cascade / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / external side of plasma membrane / axon / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular space / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang, C. / Jiang, W. / Yang, K. / Wang, X. / Guo, Q. / Brunger, A.T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2024 Title: Structure and topography of the synaptic V-ATPase-synaptophysin complex. Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard G Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua ...Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard G Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua Jiang / Michael H B Stowell / Wolfgang Baumeister / Qiang Guo / Axel T Brunger / Abstract: Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a ...Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a well-defined interface between the synaptic vesicle V-ATPase and synaptophysin by in situ cryo-electron tomography and single-particle cryo-electron microscopy of functional synaptic vesicles isolated from mouse brains. The synaptic vesicle V-ATPase is an ATP-dependent proton pump that establishes the proton gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogues synaptoporin and synaptogyrin belong to a family of abundant synaptic vesicle proteins whose function is still unclear. We performed structural and functional studies of synaptophysin-knockout mice, confirming the identity of synaptophysin as an interaction partner with the V-ATPase. Although there is little change in the conformation of the V-ATPase upon interaction with synaptophysin, the presence of synaptophysin in synaptic vesicles profoundly affects the copy number of V-ATPases. This effect on the topography of synaptic vesicles suggests that synaptophysin assists in their biogenesis. In support of this model, we observed that synaptophysin-knockout mice exhibit severe seizure susceptibility, suggesting an imbalance of neurotransmitter release as a physiological consequence of the absence of synaptophysin. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bry.cif.gz | 527.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bry.ent.gz | 424.5 KB | Display | PDB format |
PDBx/mmJSON format | 9bry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bry_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 9bry_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 9bry_validation.xml.gz | 78.9 KB | Display | |
Data in CIF | 9bry_validation.cif.gz | 122.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/9bry ftp://data.pdbj.org/pub/pdb/validation_reports/br/9bry | HTTPS FTP |
-Related structure data
Related structure data | 44845MC 9braC 9brqC 9brrC 9brsC 9brtC 9bruC 9brzC 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
-V-type proton ATPase ... , 6 types, 14 molecules cbdghijklmnoea
#1: Protein | Mass: 51046.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: V-type proton ATPase subunit S1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1Q9 | ||||
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#2: Protein | Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: V-type proton ATPase 21 kDa proteolipid subunit / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91V37 | ||||
#3: Protein | Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: V-type proton ATPase subunit d 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51863 | ||||
#5: Protein | Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Details: V-type proton ATPase 16 kDa proteolipid subunit / Source: (natural) Mus musculus (house mouse) / References: UniProt: P63082 #7: Protein | | Mass: 9203.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: V-type proton ATPase subunit e 2 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91XE7 #8: Protein | | Mass: 96442.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: V-type proton ATPase 116 kDa subunit a isoform 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z1G4 |
-Protein , 2 types, 2 molecules fp
#4: Protein | Mass: 11000.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribonuclease kappa / Source: (natural) Mus musculus (house mouse) References: UniProt: Q8K3C0, Hydrolases; Acting on ester bonds |
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#6: Protein | Mass: 32751.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Renin receptor / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CYN9 |
-Sugars , 4 types, 8 molecules
#9: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(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 | ||||
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#10: Polysaccharide | Source method: isolated from a genetically manipulated source #11: Sugar | ChemComp-NAG / #12: Sugar | ChemComp-BMA / | |
-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: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Syptophysin gene knock-out mouse brain isolated glutamatergic synaptic vesicles Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#8 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The specimen state should be an intact subcellular component. |
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: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.21_5207: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53390 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT Details: The initial model is the model of wild-type V0-only V-ATPase. For fitting and refinement details, see https://doi.org/10.1038/s41586-024-07610-x. | ||||||||||||||||||||||||
Refine LS restraints |
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