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Yorodumi- EMDB-44842: Intact V-ATPase State 2 in synaptophysin knock-out isolated synap... -
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-Basic information
Entry | Database: EMDB / ID: EMD-44842 | |||||||||
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Title | Intact V-ATPase State 2 in synaptophysin knock-out isolated synaptic vesicles | |||||||||
Map data | Full map of V-ATPase State 2 in synaptophysin knock-out ISVs. | |||||||||
Sample |
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Keywords | V-ATPase / synaptic vesicle / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / eye pigmentation / Insulin receptor recycling / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / RHOA GTPase cycle / rostrocaudal neural tube patterning ...Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / eye pigmentation / Insulin receptor recycling / central nervous system maturation / transporter activator activity / negative regulation of autophagic cell death / RHOA GTPase cycle / rostrocaudal neural tube patterning / Metabolism of Angiotensinogen to Angiotensins / 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 / proton-transporting V-type ATPase, V0 domain / extrinsic component of synaptic vesicle membrane / P-type proton-exporting transporter activity / ROS and RNS production in phagocytes / intracellular organelle / plasma membrane proton-transporting V-type ATPase complex / lysosomal lumen acidification / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuolar transport / proton-transporting V-type ATPase complex / head morphogenesis / vacuolar proton-transporting V-type ATPase complex / protein localization to cilium / vacuolar acidification / dendritic spine membrane / regulation of cellular pH / osteoclast development / ATPase complex / ATPase activator activity / autophagosome membrane / microvillus / regulation of MAPK cascade / transmembrane transporter complex / cilium assembly / positive regulation of Wnt signaling pathway / angiotensin maturation / regulation of macroautophagy / endomembrane system / axon terminus / ATP metabolic process / H+-transporting two-sector ATPase / proton transmembrane transport / phagocytic vesicle / RNA endonuclease activity / ruffle / 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 / 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 / early endosome / positive regulation of ERK1 and ERK2 cascade / 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 | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Wang C / Jiang W / Yang K / Wang X / Guo Q / Brunger AT | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44842.map.gz | 321.4 MB | EMDB map data format | |
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Header (meta data) | emd-44842-v30.xml emd-44842.xml | 37.8 KB 37.8 KB | Display Display | EMDB header |
Images | emd_44842.png | 118.2 KB | ||
Filedesc metadata | emd-44842.cif.gz | 9.7 KB | ||
Others | emd_44842_additional_1.map.gz emd_44842_additional_2.map.gz emd_44842_half_map_1.map.gz emd_44842_half_map_2.map.gz | 318.4 MB 274.4 MB 274.1 MB 274.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44842 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44842 | HTTPS FTP |
-Related structure data
Related structure data | 9brsMC 9braC 9brqC 9brrC 9brtC 9bruC 9bryC 9brzC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_44842.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Full map of V-ATPase State 2 in synaptophysin knock-out ISVs. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1064 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: EMhancer map of V-ATPase State 2 in synaptophysin knock-out ISVs.
File | emd_44842_additional_1.map | ||||||||||||
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Annotation | EMhancer map of V-ATPase State 2 in synaptophysin knock-out ISVs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_44842_additional_2.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of V-ATPase State 2 in synaptophysin knock-out ISVs.
File | emd_44842_half_map_1.map | ||||||||||||
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Annotation | Half map of V-ATPase State 2 in synaptophysin knock-out ISVs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of V-ATPase State 2 in synaptophysin knock-out ISVs.
File | emd_44842_half_map_2.map | ||||||||||||
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Annotation | Half map of V-ATPase State 2 in synaptophysin knock-out ISVs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Synaptophysin knock-out mouse brain isolated glutamatergic synapt...
+Supramolecule #1: Synaptophysin knock-out mouse brain isolated glutamatergic synapt...
+Macromolecule #1: V-type proton ATPase subunit E 1
+Macromolecule #2: V-type proton ATPase subunit G 2
+Macromolecule #3: V-type proton ATPase subunit C 1
+Macromolecule #4: V-type proton ATPase subunit H
+Macromolecule #5: V-type proton ATPase 116 kDa subunit a 1
+Macromolecule #6: V-type proton ATPase subunit e 2
+Macromolecule #7: Ribonuclease kappa
+Macromolecule #8: V-type proton ATPase subunit F
+Macromolecule #9: V-type proton ATPase subunit d 1
+Macromolecule #10: V-type proton ATPase subunit S1
+Macromolecule #11: Renin receptor cytoplasmic fragment
+Macromolecule #12: V-type proton ATPase 21 kDa proteolipid subunit c''
+Macromolecule #13: V-type proton ATPase 16 kDa proteolipid subunit c
+Macromolecule #14: V-type proton ATPase catalytic subunit A
+Macromolecule #15: V-type proton ATPase subunit B, brain isoform
+Macromolecule #16: V-type proton ATPase subunit D
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
Details | The specimen state should be an intact subcellular component. |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30487 |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-9brs: |