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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 / eye pigmentation / RHOA GTPase cycle / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / transporter activator activity / negative regulation of autophagic cell death ...Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / RHOA GTPase cycle / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / 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 / synaptic vesicle lumen acidification / endosome to plasma membrane protein transport / intracellular organelle / ROS and RNS production in phagocytes / proton-transporting V-type ATPase, V0 domain / 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 transport / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / osteoclast development / autophagosome membrane / regulation of MAPK cascade / ATPase activator activity / cilium assembly / positive regulation of Wnt signaling pathway / transmembrane transporter complex / angiotensin maturation / regulation of macroautophagy / endomembrane system / axon terminus / proton transmembrane transport / RNA endonuclease activity / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis / transmembrane transport / synaptic vesicle membrane / small GTPase binding / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / signaling receptor activity / cell body / ATPase binding / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / positive regulation of ERK1 and ERK2 cascade / early endosome / endosome membrane / endosome / nuclear speck / apical plasma membrane / lysosomal membrane / axon / external side of plasma membrane / centrosome / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / extracellular space / membrane / plasma membrane / cytoplasm / cytosol 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 Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua Jiang ...Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard 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 protein gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogs 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 | 527.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bry.ent.gz | 424.4 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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