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- PDB-9brs: Intact V-ATPase State 2 in synaptophysin knock-out isolated synap... -

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Basic information

Entry
Database: PDB / ID: 9brs
TitleIntact V-ATPase State 2 in synaptophysin knock-out isolated synaptic vesicles
Components
  • (V-type proton ATPase ...) x 14
  • Renin receptor cytoplasmic fragment
  • Ribonuclease kappa
KeywordsMEMBRANE PROTEIN / V-ATPase / synaptic vesicle
Function / homology
Function and homology information


Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / transporter activator activity / rostrocaudal neural tube patterning / RHOA GTPase cycle ...Ion channel transport / Amino acids regulate mTORC1 / Transferrin endocytosis and recycling / Insulin receptor recycling / eye pigmentation / central nervous system maturation / Metabolism of Angiotensinogen to Angiotensins / transporter activator activity / rostrocaudal neural tube patterning / RHOA GTPase cycle / positive regulation of transforming growth factor beta1 production / cellular response to increased oxygen levels / proton-transporting V-type ATPase, V1 domain / ROS and RNS production in phagocytes / synaptic vesicle lumen acidification / proton-transporting V-type ATPase, V0 domain / P-type proton-exporting transporter activity / extrinsic component of synaptic vesicle membrane / endosome to plasma membrane protein transport / lysosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / clathrin-coated vesicle membrane / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / head morphogenesis / vacuolar proton-transporting V-type ATPase complex / osteoclast development / protein localization to cilium / vacuolar acidification / proton-transporting V-type ATPase complex / dendritic spine membrane / ATPase complex / regulation of MAPK cascade / ATPase activator activity / microvillus / autophagosome membrane / cilium assembly / positive regulation of Wnt signaling pathway / regulation of macroautophagy / ATP metabolic process / angiotensin maturation / endomembrane system / H+-transporting two-sector ATPase / receptor-mediated endocytosis of virus by host cell / ruffle / axon terminus / proton-transporting ATPase activity, rotational mechanism / Neutrophil degranulation / endoplasmic reticulum-Golgi intermediate compartment membrane / proton-transporting ATP synthase activity, rotational mechanism / RNA endonuclease activity / receptor-mediated endocytosis / proton transmembrane transport / secretory granule / cilium / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of canonical Wnt signaling pathway / melanosome / apical part of cell / myelin sheath / signaling receptor activity / ATPase binding / intracellular iron ion homeostasis / postsynaptic membrane / Hydrolases; Acting on ester bonds / early endosome / lysosome / endosome / endosome membrane / nuclear speck / apical plasma membrane / axon / lysosomal membrane / external side of plasma membrane / centrosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / 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 catalytic subunit A / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit D / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit H / Ribonuclease kappa / V-type proton ATPase 21 kDa proteolipid subunit c'' / V-type proton ATPase subunit e 2 ...V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit E 1 / V-type proton ATPase subunit d 1 / V-type proton ATPase subunit D / V-type proton ATPase subunit B, brain isoform / V-type proton ATPase 16 kDa proteolipid subunit c / V-type proton ATPase subunit H / Ribonuclease kappa / V-type proton ATPase 21 kDa proteolipid subunit c'' / V-type proton ATPase subunit e 2 / Renin receptor / V-type proton ATPase subunit F / V-type proton ATPase subunit S1 / V-type proton ATPase subunit G 2 / V-type proton ATPase subunit C 1 / V-type proton ATPase 116 kDa subunit a 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsWang, C. / Jiang, W. / Yang, K. / Wang, X. / Guo, Q. / Brunger, A.T.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)RO1MH63105 United States
CitationJournal: 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 G Held / Daniel J Adams / Tamara Basta / Lucas Hampton / Ruiqi Jian / Lihua ...Authors: Chuchu Wang / Wenhong Jiang / Jeremy Leitz / Kailu Yang / Luis Esquivies / Xing Wang / Xiaotao Shen / Richard G 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 proton gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogues 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
DepositionMay 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 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 / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
8: V-type proton ATPase subunit E 1
9: V-type proton ATPase subunit E 1
Q: V-type proton ATPase subunit E 1
R: V-type proton ATPase subunit G 2
T: V-type proton ATPase subunit G 2
V: V-type proton ATPase subunit G 2
6: V-type proton ATPase subunit C 1
U: V-type proton ATPase subunit H
a: V-type proton ATPase 116 kDa subunit a 1
e: V-type proton ATPase subunit e 2
f: Ribonuclease kappa
X: V-type proton ATPase subunit F
d: V-type proton ATPase subunit d 1
c: V-type proton ATPase subunit S1
p: Renin receptor cytoplasmic fragment
b: V-type proton ATPase 21 kDa proteolipid subunit c''
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
1: V-type proton ATPase catalytic subunit A
2: V-type proton ATPase catalytic subunit A
0: V-type proton ATPase catalytic subunit A
4: V-type proton ATPase subunit B, brain isoform
5: V-type proton ATPase subunit B, brain isoform
3: V-type proton ATPase subunit B, brain isoform
7: V-type proton ATPase subunit D


Theoretical massNumber of molelcules
Total (without water)1,047,45632
Polymers1,047,45632
Non-polymers00
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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V-type proton ATPase ... , 14 types, 30 molecules 89QRTV6UaeXdcbghijklmno1204537

#1: Protein V-type proton ATPase subunit E 1 / V-ATPase subunit E 1 / V-ATPase 31 kDa subunit / p31 / Vacuolar proton pump subunit E 1


Mass: 26196.449 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: VATE1_MOUSE V-type proton ATPase subunit E 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: P50518
#2: Protein V-type proton ATPase subunit G 2 / V-ATPase subunit G 2 / V-ATPase 13 kDa subunit 2 / Vacuolar proton pump subunit G 2


Mass: 13674.476 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: VATG2_MOUSE V-type proton ATPase subunit G 2 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WTT4
#3: Protein V-type proton ATPase subunit C 1 / V-ATPase subunit C 1 / Vacuolar proton pump subunit C 1


Mass: 43945.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VATC1_MOUSE V-type proton ATPase subunit C 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z1G3
#4: Protein V-type proton ATPase subunit H / V-ATPase subunit H / Vacuolar proton pump subunit H


Mass: 55922.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VATH_MOUSE V-type proton ATPase subunit H / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BVE3
#5: 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: 96442.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: VPP1_MOUSE V-type proton ATPase 116 kDa subunit a isoform 1
Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9Z1G4
#6: 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 / Details: VA0E2_MOUSE V-type proton ATPase subunit e 2 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91XE7
#8: 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 / Details: VATF_MOUSE V-type proton ATPase subunit F / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D1K2
#9: Protein V-type proton ATPase subunit d 1 / V-ATPase subunit d 1 / P39 / Physophilin / V-ATPase 40 kDa accessory protein / V-ATPase AC39 ...V-ATPase subunit d 1 / P39 / Physophilin / V-ATPase 40 kDa accessory protein / V-ATPase AC39 subunit / Vacuolar proton pump subunit d 1


Mass: 40341.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VA0D1_MOUSE V-type proton ATPase subunit d 1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51863
#10: Protein V-type proton ATPase subunit S1 / V-ATPase subunit S1 / Protein C7-1 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / ...V-ATPase subunit S1 / Protein C7-1 / V-ATPase Ac45 subunit / V-ATPase S1 accessory protein / Vacuolar proton pump subunit S1


Mass: 51046.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VAS1_MOUSE V-type proton ATPase subunit S1 / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1Q9
#12: Protein V-type proton ATPase 21 kDa proteolipid subunit c'' / V-ATPase 21 kDa proteolipid subunit c'' / 23 kDa subunit of V-ATPase / Vacuolar proton pump 21 kDa ...V-ATPase 21 kDa proteolipid subunit c'' / 23 kDa subunit of V-ATPase / Vacuolar proton pump 21 kDa proteolipid subunit c''


Mass: 21618.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: VATO_MOUSE V-type proton ATPase 21 kDa proteolipid subunit
Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91V37
#13: Protein
V-type proton ATPase 16 kDa proteolipid subunit c / V-ATPase 16 kDa proteolipid subunit c / PL16 / Vacuolar proton pump 16 kDa proteolipid subunit c


Mass: 15815.833 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Details: VATL_MOUSE V-type proton ATPase 16 kDa proteolipid subunit
Source: (natural) Mus musculus (house mouse) / References: UniProt: P63082
#14: Protein V-type proton ATPase catalytic subunit A / V-ATPase subunit A / V-ATPase 69 kDa subunit / Vacuolar proton pump subunit alpha


Mass: 68402.875 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: VATA_MOUSE V-type proton ATPase catalytic subunit A
Source: (natural) Mus musculus (house mouse)
References: UniProt: P50516, H+-transporting two-sector ATPase
#15: 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 / Details: VATB2_MOUSE V-type proton ATPase subunit B / Source: (natural) Mus musculus (house mouse) / References: UniProt: P62814
#16: Protein V-type proton ATPase subunit D / V-ATPase subunit D / V-ATPase 28 kDa accessory protein / Vacuolar proton pump subunit D


Mass: 28419.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VATD_MOUSE V-type proton ATPase subunit D / Source: (natural) Mus musculus (house mouse) / References: UniProt: P57746

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Protein , 2 types, 2 molecules fp

#7: Protein Ribonuclease kappa / RNase K / RNase kappa / V-type proton ATPase subunit f / V-ATPase subunit f


Mass: 11000.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RNK_MOUSE Ribonuclease kappa / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8K3C0, Hydrolases; Acting on ester bonds
#11: Protein Renin receptor cytoplasmic fragment


Mass: 39128.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RENR_MOUSE Renin receptor / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CYN9

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Synaptophysin knock-out mouse brain isolated glutamatergic synaptic vesicles
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The specimen state should be an intact subcellular component.
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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.21.1_5286: / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30487 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00566773
ELECTRON MICROSCOPYf_angle_d0.76890244
ELECTRON MICROSCOPYf_dihedral_angle_d5.3369103
ELECTRON MICROSCOPYf_chiral_restr0.04510230
ELECTRON MICROSCOPYf_plane_restr0.00711573

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