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- EMDB-44354: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-44354
TitleSynaptic Vesicle V-ATPase with synaptophysin and SidK, State 2
Map data
Sample
  • Complex: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2
KeywordsMembrane / Native / Complex / Synaptic / PROTON TRANSPORT
Function / homology
Function and homology information


regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation ...regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / negative regulation of autophagic cell death / plasma membrane proton-transporting V-type ATPase complex / Insulin receptor recycling / RHOA GTPase cycle / eye pigmentation / central nervous system maturation / rostrocaudal neural tube patterning / cellular response to increased oxygen levels / regulation of synaptic vesicle priming / proton-transporting V-type ATPase, V1 domain / positive regulation of transforming growth factor beta1 production / transporter activator activity / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / P-type proton-exporting transporter activity / extrinsic component of synaptic vesicle membrane / vacuolar transport / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V0 domain / lysosomal lumen acidification / endosomal lumen acidification / neuron spine / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / osteoclast development / head morphogenesis / protein localization to cilium / regulation of short-term neuronal synaptic plasticity / vacuolar acidification / neuron projection terminus / dendritic spine membrane / regulation of cellular pH / syntaxin-1 binding / ROS and RNS production in phagocytes / Neutrophil degranulation / cholesterol binding / ATPase complex / response to amyloid-beta / ATPase activator activity / microvillus / presynaptic active zone / regulation of MAPK cascade / regulation of neuronal synaptic plasticity / autophagosome membrane / excitatory synapse / cilium assembly / positive regulation of Wnt signaling pathway / regulation of macroautophagy / ATP metabolic process / H+-transporting two-sector ATPase / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / ruffle / axon terminus / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / receptor-mediated endocytosis / SH2 domain binding / SNARE binding / secretory granule / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / neuromuscular junction / Schaffer collateral - CA1 synapse / small GTPase binding / transmembrane transport / synaptic vesicle membrane / endocytosis / positive regulation of canonical Wnt signaling pathway / apical part of cell / synaptic vesicle / melanosome / presynapse / signaling receptor activity / presynaptic membrane / ATPase binding / cell body / postsynaptic membrane / intracellular iron ion homeostasis / early endosome / lysosome / positive regulation of ERK1 and ERK2 cascade / neuron projection / postsynaptic density / endosome / endosome membrane / cilium / apical plasma membrane / protein domain specific binding
Similarity search - Function
Synaptophysin/synaptoporin / Synaptophysin / synaptoporin signature. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like ...Synaptophysin/synaptoporin / Synaptophysin / synaptoporin signature. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / ATPase, V0 complex, subunit e1/e2, metazoa / V0 complex accessory subunit Ac45 / V-type proton ATPase subunit S1, luminal domain / V-type proton ATPase subunit S1, luminal domain / Renin receptor-like / Renin receptor-like transmembrane spanning segment / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A / : / V-type proton ATPase subunit f-like / Ribonuclease kappa / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / ATPase, V1 complex, subunit D / V-type ATPase subunit E / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / ATP synthase (E/31 kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
V-type proton ATPase subunit H / Rnasek protein / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit S1 / Synaptophysin / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit F / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c ...V-type proton ATPase subunit H / Rnasek protein / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit S1 / Synaptophysin / V-type proton ATPase 116 kDa subunit a 1 / V-type proton ATPase subunit F / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit e 2 / V-type proton ATPase subunit C 1 / V-type proton ATPase subunit / Type IV secretion protein Dot / Renin receptor / V-type proton ATPase subunit D / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit G
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsCoupland CE / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
CitationJournal: Science / Year: 2024
Title: High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles.
Authors: Claire E Coupland / Ryan Karimi / Stephanie A Bueler / Yingke Liang / Gautier M Courbon / Justin M Di Trani / Cassandra J Wong / Rayan Saghian / Ji-Young Youn / Lu-Yang Wang / John L Rubinstein /
Abstract: Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or ...Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single-particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in a loss of the V region of V-ATPase from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.
History
DepositionMar 31, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44354.png

Downloads & links

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Map

FileDownload / File: emd_44354.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 384 pix.
= 527.36 Å		1.37 Å/pix.
x 384 pix.
= 527.36 Å		1.37 Å/pix.
x 384 pix.
= 527.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.124
Minimum - Maximum-0.41102564 - 0.79858476
Average (Standard dev.)0.000102959755 (±0.027345095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44354_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_44354_half_map_2.map
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Sample components

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Entire : Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2

EntireName: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2
Components
  • Complex: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2

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Supramolecule #1: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2

SupramoleculeName: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 37.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123220
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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