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- PDB-6o7u: Saccharomyces cerevisiae V-ATPase Stv1-VO -

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Basic information

Entry
Database: PDB / ID: 6o7u
TitleSaccharomyces cerevisiae V-ATPase Stv1-VO
Components
  • (V-type proton ATPase subunit ...) x 6
  • Putative protein YPR170W-B
  • V0 assembly protein 1
KeywordsMEMBRANE PROTEIN / Proton pump
Function / homology
Function and homology information


cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / vacuolar transport / endosomal lumen acidification ...cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / P-type proton-exporting transporter activity / vacuolar transport / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V0 domain / protein targeting to vacuole / vacuole organization / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification / fungal-type vacuole membrane / phosphatidylinositol-4-phosphate binding / proton transmembrane transporter activity / intracellular copper ion homeostasis / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / RNA endonuclease activity / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / late endosome / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / endosome membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / membrane
Similarity search - Function
Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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 ...Ribonuclease kappa / V-type proton ATPase subunit S1/VOA1, transmembrane domain / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / 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-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
V-type proton ATPase subunit f / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / V-type proton ATPase subunit d / V-type proton ATPase subunit c' / V-type proton ATPase subunit a, Golgi isoform / V0 assembly protein 1 / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVasanthakumar, T. / Bueler, S.A. / Wu, D. / Beilsten-Edmands, V. / Robinson, C.V. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP81294 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structural comparison of the vacuolar and Golgi V-ATPases from .
Authors: Thamiya Vasanthakumar / Stephanie A Bueler / Di Wu / Victoria Beilsten-Edmands / Carol V Robinson / John L Rubinstein /
Abstract: Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal ...Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are differentially targeted to various intracellular compartments or tissues, but how these subunit isoforms influence enzyme activity is not clear. In the yeast , isoform diversity is limited to two different versions of the proton-translocating subunit a: Vph1p, which is targeted to the vacuole, and Stv1p, which is targeted to the Golgi apparatus and endosomes. We show that purified V-ATPase complexes containing Vph1p have higher ATPase activity than complexes containing Stv1p and that the relative difference in activity depends on the presence of lipids. We also show that V complexes containing Stv1p could be readily purified without attached V regions. We used this effect to determine structures of the membrane-embedded V region with Stv1p at 3.1-Å resolution, which we compare with a structure of the V region with Vph1p that we determine to 3.2-Å resolution. These maps reveal differences in the surface charge near the cytoplasmic proton half-channel. Both maps also show the presence of bound lipids, as well as regularly spaced densities that may correspond to ergosterol or bound detergent, around the c-ring.
History
DepositionMar 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _pdbx_audit_support.funding_organization
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
a: V-type proton ATPase subunit a, Golgi isoform
b: V0 assembly protein 1
c: V-type proton ATPase subunit c''
d: V-type proton ATPase subunit d
e: V-type proton ATPase subunit e
f: Putative protein YPR170W-B
g: V-type proton ATPase subunit c
h: V-type proton ATPase subunit c
i: V-type proton ATPase subunit c
j: V-type proton ATPase subunit c
k: V-type proton ATPase subunit c
l: V-type proton ATPase subunit c
m: V-type proton ATPase subunit c
n: V-type proton ATPase subunit c
o: V-type proton ATPase subunit c'


Theoretical massNumber of molelcules
Total (without water)362,27315
Polymers362,27315
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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V-type proton ATPase subunit ... , 6 types, 13 molecules acdeghijklmno

#1: Protein V-type proton ATPase subunit a, Golgi isoform / V-ATPase a 2 subunit / Similar to VPH1 protein 1 / V-ATPase 101 kDa subunit / V-ATPase subunit ...V-ATPase a 2 subunit / Similar to VPH1 protein 1 / V-ATPase 101 kDa subunit / V-ATPase subunit AC115 / Vacuolar proton translocating ATPase subunit a 2


Mass: 104481.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P37296
#3: Protein V-type proton ATPase subunit c'' / V-ATPase subunit c'' / V-ATPase 22 kDa proteolipid subunit / Vacuolar proton pump c'' subunit


Mass: 22610.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23968
#4: Protein V-type proton ATPase subunit d / V-ATPase subunit d / V-ATPase 39 kDa subunit / V-ATPase subunit M39 / Vacuolar proton pump subunit d


Mass: 39822.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32366
#5: Protein V-type proton ATPase subunit e / V-ATPase subunit e / Low dye-binding protein 10 / Vacuolar proton pump subunit e


Mass: 8387.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q3E7B6
#7: Protein
V-type proton ATPase subunit c / V-ATPase subunit c / Guanine nucleotide exchange factor 2 / V-ATPase 16 kDa proteolipid subunit 1 / ...V-ATPase subunit c / Guanine nucleotide exchange factor 2 / V-ATPase 16 kDa proteolipid subunit 1 / Vacuolar proton pump c subunit


Mass: 16357.501 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25515
#8: Protein V-type proton ATPase subunit c' / V-ATPase subunit c' / Proteolipid protein VMA11 / Trifluoperazine resistance protein 3 / V-ATPase ...V-ATPase subunit c' / Proteolipid protein VMA11 / Trifluoperazine resistance protein 3 / V-ATPase 16 kDa proteolipid subunit 2 / Vacuolar proton pump c' subunit


Mass: 17046.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32842

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Protein , 2 types, 2 molecules bf

#2: Protein V0 assembly protein 1


Mass: 29694.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53262
#6: Protein Putative protein YPR170W-B


Mass: 9369.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P0C5R9

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Details

Sequence detailsAuthors state that the C-terminal 3XFLAG tag of V-type proton ATPase subunit a was incorporated ...Authors state that the C-terminal 3XFLAG tag of V-type proton ATPase subunit a was incorporated into the chromosome of S. cerevisiae by homologous recombination.

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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: Saccharomyces cerevisiae V-ATPase Stv1-VO / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 42.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163024 / Symmetry type: POINT

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