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- PDB-9b8p: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 -

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Basic information

Entry
Database: PDB / ID: 9b8p
TitleSynaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1
Components
  • (V-type proton ATPase subunit ...) x 4
  • ATPase H+-transporting V1 subunit D
  • H(+)-transporting two-sector ATPase
  • SidK
KeywordsPROTON TRANSPORT / Mmebrane / Synaptic / Complex
Function / homology
Function and homology information


Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / symbiont-mediated suppression of host phagosome acidification / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / P-type proton-exporting transporter activity / extrinsic component of synaptic vesicle membrane / cellular response to increased oxygen levels ...Ion channel transport / Transferrin endocytosis and recycling / Amino acids regulate mTORC1 / symbiont-mediated suppression of host phagosome acidification / Insulin receptor recycling / proton-transporting V-type ATPase, V1 domain / synaptic vesicle lumen acidification / P-type proton-exporting transporter activity / extrinsic component of synaptic vesicle membrane / cellular response to increased oxygen levels / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / proton-transporting V-type ATPase complex / protein localization to cilium / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / regulation of cellular pH / ROS and RNS production in phagocytes / Neutrophil degranulation / ATPase complex / microvillus / proton-transporting ATPase activity, rotational mechanism / cilium assembly / H+-transporting two-sector ATPase / ATP metabolic process / ruffle / proton transmembrane transport / secretory granule / synaptic vesicle membrane / melanosome / ATPase binding / intracellular iron ion homeostasis / endosome / cilium / apical plasma membrane / centrosome / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ATPase, V1 complex, subunit A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / 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 A / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / 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 / : / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit F / V-type proton ATPase subunit B, brain isoform / Type IV secretion protein Dot / V-type proton ATPase subunit D / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit G
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCoupland, E.M. / Rubinstein, J.L.
Funding support Canada, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H(+)-transporting two-sector ATPase
B: H(+)-transporting two-sector ATPase
C: H(+)-transporting two-sector ATPase
D: V-type proton ATPase subunit B, brain isoform
E: V-type proton ATPase subunit B, brain isoform
F: V-type proton ATPase subunit B, brain isoform
H: ATPase H+-transporting V1 subunit D
I: V-type proton ATPase subunit E 1
J: V-type proton ATPase subunit E 1
K: V-type proton ATPase subunit E 1
L: V-type proton ATPase subunit F
M: V-type proton ATPase subunit G
N: V-type proton ATPase subunit G
O: V-type proton ATPase subunit G
Q: SidK
R: SidK
S: SidK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)742,55018
Polymers742,12317
Non-polymers4271
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 7 molecules ABCHQRS

#1: Protein H(+)-transporting two-sector ATPase


Mass: 71483.438 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: D4A133, H+-transporting two-sector ATPase
#3: Protein ATPase H+-transporting V1 subunit D / ATPase / H+ transporting / V1 subunit D / isoform CRA_c / lysosomal V1 subunit D


Mass: 28359.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P503
#7: Protein SidK


Mass: 65505.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZWW6

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V-type proton ATPase subunit ... , 4 types, 10 molecules DEFIJKLMNO

#2: Protein V-type proton ATPase subunit B, brain isoform / V-ATPase subunit B 2 / Endomembrane proton pump 58 kDa subunit / Vacuolar proton pump subunit B 2


Mass: 56611.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62815
#4: Protein V-type proton ATPase subunit E 1 / V-ATPase subunit E 1 / Vacuolar proton pump subunit E 1


Mass: 26167.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6PCU2
#5: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar proton pump subunit F


Mass: 13389.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P50408
#6: Protein V-type proton ATPase subunit G


Mass: 13690.476 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q8R2H0

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Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1
Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 37.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198533 / Symmetry type: POINT

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