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- EMDB-44353: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-44353
TitleSynaptic Vesicle V-ATPase with synaptophysin and SidK, State 3
Map data
Sample
  • Complex: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3
KeywordsComplex / Membrane / Native / Synaptic / PROTON TRANSPORT
Function / homology
Function and homology information


vestibular calyx terminal / regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / symbiont-mediated suppression of host phagosome acidification / Insulin receptor recycling / RHOA GTPase cycle / negative regulation of autophagic cell death ...vestibular calyx terminal / regulation of opioid receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / symbiont-mediated suppression of host phagosome acidification / Insulin receptor recycling / RHOA GTPase cycle / negative regulation of autophagic cell death / eye pigmentation / central nervous system maturation / proton-transporting V-type ATPase, V1 domain / positive regulation of transforming growth factor beta1 production / rostrocaudal neural tube patterning / synaptic vesicle lumen acidification / lysosomal lumen acidification / regulation of synaptic vesicle priming / P-type proton-exporting transporter activity / osteoclast development / proton-transporting V-type ATPase, V0 domain / cellular response to increased oxygen levels / extrinsic component of synaptic vesicle membrane / endosome to plasma membrane protein transport / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / clathrin-coated vesicle membrane / basal part of cell / head morphogenesis / vacuolar proton-transporting V-type ATPase complex / neuron spine / regulation of short-term neuronal synaptic plasticity / vacuolar acidification / : / ROS and RNS production in phagocytes / dendritic spine membrane / syntaxin-1 binding / Neutrophil degranulation / presynaptic active zone / cholesterol binding / neuron projection terminus / response to amyloid-beta / homeostatic process / microvillus / regulation of neuronal synaptic plasticity / autophagosome membrane / regulation of MAPK cascade / proton-transporting ATPase activity, rotational mechanism / positive regulation of Wnt signaling pathway / H+-transporting two-sector ATPase / ATP metabolic process / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / regulation of macroautophagy / ruffle / RNA endonuclease activity / endoplasmic reticulum-Golgi intermediate compartment membrane / proton transmembrane transport / receptor-mediated endocytosis / SH2 domain binding / excitatory synapse / molecular function activator activity / SNARE binding / neuromuscular junction / regulation of long-term neuronal synaptic plasticity / protein homooligomerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / small GTPase binding / endocytosis / apical part of cell / positive regulation of canonical Wnt signaling pathway / terminal bouton / melanosome / synaptic vesicle / synaptic vesicle membrane / ATPase binding / presynapse / signaling receptor activity / cell body / presynaptic membrane / intracellular iron ion homeostasis / positive regulation of ERK1 and ERK2 cascade / lysosome / endosome / apical plasma membrane / endosome membrane / neuron projection / postsynaptic density / external side of plasma membrane / protein domain specific binding / axon / lysosomal membrane / ubiquitin protein ligase binding / synapse / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm
Similarity search - Function
Synaptophysin/synaptoporin / Synaptophysin / synaptoporin signature. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / BIG1 N-terminal domain / 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 ...Synaptophysin/synaptoporin / Synaptophysin / synaptoporin signature. / Marvel domain / Membrane-associating domain / MARVEL domain profile. / BIG1 N-terminal domain / 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 / Renin receptor N-terminal domain / 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 / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Ribonuclease kappa / : / V-type proton ATPase subunit f-like / Vacuolar (H+)-ATPase G subunit / V-type proton ATPase subunit S1/VOA1, transmembrane domain / Vacuolar (H+)-ATPase G subunit / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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 / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-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 / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like 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 / Ribonuclease K / V-type proton ATPase 21 kDa proteolipid subunit c'' / 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 / Ribonuclease K / V-type proton ATPase 21 kDa proteolipid subunit c'' / 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 / Uncharacterized protein / 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: 3.5 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_44353.png

Downloads & links

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Map

FileDownload / File: emd_44353.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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: 0.185
Minimum - Maximum-0.951793 - 1.5873989
Average (Standard dev.)0.00012936867 (±0.03976526)
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: #2

Fileemd_44353_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_44353_half_map_2.map
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Sample components

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Entire : Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3

EntireName: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3
Components
  • Complex: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3

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Supramolecule #1: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3

SupramoleculeName: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3
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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 198533
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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