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Yorodumi- PDB-9bra: Intact V-ATPase State 2 and synaptophysin complex in mouse brain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bra | |||||||||
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Title | Intact V-ATPase State 2 and synaptophysin complex in mouse brain isolated synaptic vesicles | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / V-ATPase / synaptic vesicle | |||||||||
Function / homology | Function and homology information Ion channel transport / regulation of opioid receptor signaling pathway / Amino acids regulate mTORC1 / clathrin-sculpted glutamate transport vesicle membrane / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / RHOA GTPase cycle / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins ...Ion channel transport / regulation of opioid receptor signaling pathway / Amino acids regulate mTORC1 / clathrin-sculpted glutamate transport vesicle membrane / 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 / proton-transporting V-type ATPase, V1 domain / 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 / 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 / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 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 / vacuolar acidification / syntaxin-1 binding / osteoclast development / regulation of synaptic vesicle exocytosis / : / cholesterol binding / ATPase complex / presynaptic active zone / regulation of neuronal synaptic plasticity / autophagosome membrane / microvillus / regulation of MAPK cascade / ATPase activator activity / synaptic vesicle endocytosis / excitatory synapse / cilium assembly / positive regulation of Wnt signaling pathway / transmembrane transporter complex / angiotensin maturation / regulation of macroautophagy / endomembrane system / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / RNA endonuclease activity / phagocytic vesicle / Neutrophil degranulation / 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 / cilium / synaptic vesicle membrane / small GTPase binding / endocytosis / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / presynapse / apical part of cell / myelin sheath / presynaptic membrane / signaling receptor activity / cell body / ATPase binding / chemical synaptic transmission / postsynaptic membrane / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / Hydrolases; Acting on ester bonds / postsynaptic density Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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 | 9bra.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9bra.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9bra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bra_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 9bra_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 9bra_validation.xml.gz | 196.2 KB | Display | |
Data in CIF | 9bra_validation.cif.gz | 310.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/9bra ftp://data.pdbj.org/pub/pdb/validation_reports/br/9bra | HTTPS FTP |
-Related structure data
Related structure data | 44839MC 9brqC 9brrC 9brsC 9brtC 9bruC 9bryC 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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-Components
-V-type proton ATPase ... , 14 types, 30 molecules 89QRTV01234567UXabdghijklmnoce
#1: Protein | Mass: 26196.449 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: VATE1_MOUSE V-type proton ATPase subunit E 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: P50518 #2: Protein | Mass: 13674.476 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: VATG2_MOUSE V-type proton ATPase subunit G 2 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WTT4 #3: Protein | Mass: 68402.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: VATA_MOUSE V-type proton ATPase catalytic subunit A Source: (natural) Mus musculus (house mouse) References: UniProt: P50516, H+-transporting two-sector ATPase #4: Protein | Mass: 56611.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: VATB2_MOUSE V-type proton ATPase subunit B / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62814 #5: Protein | | Mass: 43945.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VATC1_MOUSE V-type proton ATPase subunit C 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z1G3 #6: Protein | | Mass: 28419.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VATD_MOUSE V-type proton ATPase subunit D / Source: (natural) Mus musculus (house mouse) / References: UniProt: P57746 #7: Protein | | Mass: 55922.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VATH_MOUSE V-type proton ATPase subunit H / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BVE3 #8: Protein | | Mass: 13389.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VATF_MOUSE V-type proton ATPase subunit F / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1K2 #9: Protein | | Mass: 96442.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: VPP1_MOUSE V-type proton ATPase 116 kDa subunit a isoform 1 Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z1G4 #10: Protein | | Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: VATO_MOUSE V-type proton ATPase 21 kDa proteolipid subunit Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91V37 #11: Protein | | Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VA0D1_MOUSE V-type proton ATPase subunit d 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51863 #12: Protein | Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source Details: VATL_MOUSE V-type proton ATPase 16 kDa proteolipid subunit Source: (natural) Mus musculus (house mouse) / References: UniProt: P63082 #14: Protein | | Mass: 51046.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VAS1_MOUSE V-type proton ATPase subunit S1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1Q9 #17: Protein | | Mass: 9203.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VA0E2_MOUSE V-type proton ATPase subunit e 2 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91XE7 |
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-Protein , 3 types, 3 molecules pfs
#13: Protein | Mass: 39128.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RENR_MOUSE Renin receptor / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CYN9 |
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#15: Protein | Mass: 11000.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNK_MOUSE Ribonuclease kappa / Source: (natural) Mus musculus (house mouse) References: UniProt: Q8K3C0, Hydrolases; Acting on ester bonds |
#16: Protein | Mass: 34045.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SYPH_MOUSE Synaptophysin / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q62277 |
-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: Mouse brain isolated glutamatergic synaptic vesicles / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / 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: 4000 nm / Nominal defocus min: 1000 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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25667 / Symmetry type: POINT | |||||||||
Atomic model building | Protocol: FLEXIBLE FIT |