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- PDB-9brs: Intact V-ATPase State 2 in synaptophysin knock-out isolated synap... -
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Basic information
Entry | Database: PDB / ID: 9brs | |||||||||
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Title | Intact V-ATPase State 2 in synaptophysin knock-out isolated synaptic vesicles | |||||||||
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![]() | MEMBRANE PROTEIN / V-ATPase / synaptic vesicle | |||||||||
Function / homology | ![]() 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 / 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 / head morphogenesis / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / osteoclast development / ATPase complex / autophagosome membrane / microvillus / 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 / 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 / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule / transmembrane transport / cilium / synaptic vesicle membrane / small GTPase binding / endocytosis / melanosome / positive regulation of canonical Wnt signaling pathway / synaptic vesicle / apical part of cell / myelin sheath / 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 / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / nucleoplasm / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
![]() | Wang, C. / Jiang, W. / Yang, K. / Wang, X. / Guo, Q. / Brunger, A.T. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 196 KB | Display | |
Data in CIF | ![]() | 307.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 44842MC ![]() 9braC ![]() 9brqC ![]() 9brrC ![]() 9brtC ![]() 9bruC ![]() 9bryC ![]() 9brzC 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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Components
-V-type proton ATPase ... , 14 types, 30 molecules 89QRTV6UaeXdcbghijklmno1204537
#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) ![]() ![]() #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) ![]() ![]() #3: 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) ![]() ![]() #4: 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) ![]() ![]() #5: 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) ![]() ![]() #6: 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) ![]() ![]() #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) ![]() ![]() #9: 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) ![]() ![]() #10: 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) ![]() ![]() #12: 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) ![]() ![]() #13: 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) ![]() ![]() #14: 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) ![]() ![]() References: UniProt: P50516, H+-transporting two-sector ATPase #15: 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) ![]() ![]() #16: 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) ![]() ![]() |
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-Protein , 2 types, 2 molecules fp
#7: Protein | Mass: 11000.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNK_MOUSE Ribonuclease kappa / Source: (natural) ![]() ![]() References: UniProt: Q8K3C0, Hydrolases; Acting on ester bonds |
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#11: Protein | Mass: 39128.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RENR_MOUSE Renin receptor / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Synaptophysin knock-out 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: ![]() ![]() |
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 |
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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: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.21.1_5286: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30487 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||
Refine LS restraints |
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