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- PDB-9b8o: Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo -

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Entry
Database: PDB / ID: 9b8o
TitleSynaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, Vo
Components
  • (V-type proton ATPase ...) x 6
  • ATPase H+-transporting V1 subunit D
  • ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
  • Renin receptor
  • Rnasek protein
  • Synaptophysin
KeywordsPROTON TRANSPORT / Membrane / Synaptic / Complex
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 / positive regulation of transforming growth factor beta1 production / transporter activator activity / proton-transporting V-type ATPase, V0 domain / synaptic vesicle lumen acidification / 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 / response to amyloid-beta / ATPase activator activity / 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 / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / axon terminus / proton-transporting ATPase activity, rotational mechanism / endoplasmic reticulum-Golgi intermediate compartment membrane / RNA endonuclease activity / proton transmembrane transport / receptor-mediated endocytosis / SH2 domain binding / SNARE binding / 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 / 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 / axon / external side of plasma membrane / lysosomal membrane / synapse / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex
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 / : / V-type proton ATPase subunit f-like / Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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 / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
CHOLESTEROL / Chem-LP3 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PHOSPHATIDYLETHANOLAMINE / Chem-WJP / Rnasek protein / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / V-type proton ATPase subunit S1 / Synaptophysin / V-type proton ATPase 116 kDa subunit a 1 ...CHOLESTEROL / Chem-LP3 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PHOSPHATIDYLETHANOLAMINE / Chem-WJP / Rnasek protein / ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_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 16 kDa proteolipid subunit c / V-type proton ATPase subunit e 2 / V-type proton ATPase subunit / Renin receptor / V-type proton ATPase subunit D
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCoupland, C.E. / 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 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.2Jul 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
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: ATPase H+-transporting V1 subunit D
P: V-type proton ATPase subunit S1
U: Synaptophysin
a: V-type proton ATPase 116 kDa subunit a 1
b: ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a
d: V-type proton ATPase subunit
e: V-type proton ATPase subunit e 2
f: Rnasek protein
g: V-type proton ATPase 16 kDa proteolipid subunit c
h: V-type proton ATPase 16 kDa proteolipid subunit c
i: V-type proton ATPase 16 kDa proteolipid subunit c
j: V-type proton ATPase 16 kDa proteolipid subunit c
k: V-type proton ATPase 16 kDa proteolipid subunit c
l: V-type proton ATPase 16 kDa proteolipid subunit c
m: V-type proton ATPase 16 kDa proteolipid subunit c
n: V-type proton ATPase 16 kDa proteolipid subunit c
o: V-type proton ATPase 16 kDa proteolipid subunit c
p: Renin receptor
L: V-type proton ATPase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)512,03475
Polymers483,31819
Non-polymers28,71656
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 , 5 types, 5 molecules HUbfp

#1: 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
#3: Protein Synaptophysin / Major synaptic vesicle protein p38


Mass: 33331.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P07825
#5: Protein ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a / ATPase / H+ transporting / lysosomal V0 subunit B / Atp6v0b protein


Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: B0K022
#8: Protein Rnasek protein


Mass: 9502.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A8J8YMT9
#10: Protein Renin receptor / ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal- ...ATPase H(+)-transporting lysosomal accessory protein 2 / ATPase H(+)-transporting lysosomal-interacting protein 2 / Renin/prorenin receptor


Mass: 39118.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6AXS4

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V-type proton ATPase ... , 6 types, 14 molecules PadeghijklmnoL

#2: Protein V-type proton ATPase subunit S1 / V-ATPase subunit S1 / C7-1 protein / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / ...V-ATPase subunit S1 / C7-1 protein / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / Vacuolar proton pump subunit S1


Mass: 51160.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: O54715
#4: Protein V-type proton ATPase 116 kDa subunit a 1 / V-ATPase 116 kDa subunit a 1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit ...V-ATPase 116 kDa subunit a 1 / Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit / Vacuolar adenosine triphosphatase subunit Ac116 / Vacuolar proton pump subunit 1 / Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1


Mass: 94950.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P25286
#6: Protein V-type proton ATPase subunit


Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5M7T6
#7: Protein V-type proton ATPase subunit e 2 / V-ATPase subunit e 2 / Vacuolar proton pump subunit e 2


Mass: 9203.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5EB76
#9: Protein
V-type proton ATPase 16 kDa proteolipid subunit c / V-ATPase 16 kDa proteolipid subunit c / Vacuolar proton pump 16 kDa proteolipid subunit c


Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P63081
#11: 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

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Sugars , 3 types, 10 molecules

#12: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#13: Polysaccharide alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D- ...alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-2DGlcpa1-3DGlcpa1-3DManpa1-2DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1a_1-5]/1-1-2-3-3-3-4-4-4-3-3/a4-b1_b4-c1_c3-d1_c6-j1_d2-e1_e2-f1_f3-g1_g3-h1_h2-i1_j6-k1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(2+1)][a-D-Glcp]{}}}}}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#16: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 46 molecules

#14: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#15: Chemical ChemComp-WJP / methyl (3R,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen-1-yl dihydrogen diphosphate / dolichol-pp


Mass: 534.603 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C26H48O7P2
#17: Chemical ChemComp-LP3 / (7R)-4,7-DIHYDROXY-N,N,N-TRIMETHYL-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOSAN-1-AMINIUM 4-OXIDE


Mass: 524.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H55NO7P
#18: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#19: Chemical...
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C27H46O

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Details

Has ligand of interestN
Has protein modificationY

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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, Vo
Type: COMPLEX / Entity ID: #1, #11, #3, #5-#6, #9-#10 / Source: NATURAL
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Sprague Dawley / Cellular location: Synaptic Vesicle Membrane / Organ: Brain / Organelle: Synaptic Vesicle
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GRAPHENE OXIDE / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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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