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- PDB-9brr: Intact V-ATPase State 3 in synaptophysin knock-out isolated synap... -
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Basic information
Entry | Database: PDB / ID: 9brr | |||||||||
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Title | Intact V-ATPase State 3 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 / plasma membrane proton-transporting V-type ATPase complex / 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 / 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 / head morphogenesis / osteoclast development / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / dendritic spine membrane / regulation of cellular pH / vacuolar acidification / ATPase complex / autophagosome membrane / microvillus / regulation of MAPK cascade / ATPase activator activity / positive regulation of Wnt signaling pathway / cilium assembly / transmembrane transporter complex / endomembrane system / regulation of macroautophagy / angiotensin maturation / ATP metabolic process / axon terminus / H+-transporting two-sector ATPase / proton transmembrane transport / ruffle / phagocytic vesicle / RNA endonuclease activity / proton-transporting ATPase activity, rotational mechanism / Neutrophil degranulation / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / receptor-mediated endocytosis / secretory granule / transmembrane transport / cilium / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of canonical Wnt signaling pathway / melanosome / synaptic vesicle / apical part of cell / myelin sheath / signaling receptor activity / ATPase binding / cell body / 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 / external side of plasma membrane / axon / lysosomal membrane / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / 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: 4.5 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 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 44841MC ![]() 9braC ![]() 9brqC ![]() 9brsC ![]() 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 bghijklmno102345789QRTVX6Udaec
#1: 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) ![]() ![]() | ||||||||||||||||||||||||
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#2: 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) ![]() ![]() #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) ![]() ![]() 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) ![]() ![]() #5: 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) ![]() ![]() #6: 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) ![]() ![]() #7: 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) ![]() ![]() #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: 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) ![]() ![]() #10: 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) ![]() ![]() #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) ![]() ![]() #12: 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) ![]() ![]() #13: 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) ![]() ![]() #15: 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) ![]() ![]() |
-Protein , 2 types, 2 molecules fp
#14: 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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#16: 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_5207: / Classification: refinement | |||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22018 / Symmetry type: POINT | |||||||||
Atomic model building | Protocol: FLEXIBLE FIT |