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- EMDB-0645: Saccharomyces cerevisiae V-ATPase Stv1-VO -

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Basic information

Entry
Database: EMDB / ID: EMD-0645
TitleSaccharomyces cerevisiae V-ATPase Stv1-VO
Map data
Sample
  • Complex: Saccharomyces cerevisiae V-ATPase Stv1-VO
    • Protein or peptide: V-type proton ATPase subunit a, Golgi isoform
    • Protein or peptide: V0 assembly protein 1
    • Protein or peptide: V-type proton ATPase subunit c''
    • Protein or peptide: V-type proton ATPase subunit d
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: Putative protein YPR170W-B
    • Protein or peptide: V-type proton ATPase subunit c
    • Protein or peptide: V-type proton ATPase subunit c'
KeywordsProton pump / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVasanthakumar T / Bueler SA / Wu D / Beilsten-Edmands V / Robinson CV / Rubinstein JL
Funding support Canada, 1 items
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, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseApr 3, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6o7u
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_0645.png

Downloads & links

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Map

FileDownload / File: emd_0645.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-6.6416273 - 9.956531999999999
Average (Standard dev.)0.0025671786 (±0.36607447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-6.6429.9570.003

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Supplemental data

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Sample components

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Entire : Saccharomyces cerevisiae V-ATPase Stv1-VO

EntireName: Saccharomyces cerevisiae V-ATPase Stv1-VO
Components
  • Complex: Saccharomyces cerevisiae V-ATPase Stv1-VO
    • Protein or peptide: V-type proton ATPase subunit a, Golgi isoform
    • Protein or peptide: V0 assembly protein 1
    • Protein or peptide: V-type proton ATPase subunit c''
    • Protein or peptide: V-type proton ATPase subunit d
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: Putative protein YPR170W-B
    • Protein or peptide: V-type proton ATPase subunit c
    • Protein or peptide: V-type proton ATPase subunit c'

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Supramolecule #1: Saccharomyces cerevisiae V-ATPase Stv1-VO

SupramoleculeName: Saccharomyces cerevisiae V-ATPase Stv1-VO / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: V-type proton ATPase subunit a, Golgi isoform

MacromoleculeName: V-type proton ATPase subunit a, Golgi isoform / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 104.481141 KDa
SequenceString: MNQEEAIFRS ADMTYVQLYI PLEVIREVTF LLGKMSVFMV MDLNKDLTAF QRGYVNQLRR FDEVERMVGF LNEVVEKHAA ETWKYILHI DDEGNDIAQP DMADLINTME PLSLENVNDM VKEITDCESR ARQLDESLDS LRSKLNDLLE QRQVIFECSK F IEVNPGIA ...String:
MNQEEAIFRS ADMTYVQLYI PLEVIREVTF LLGKMSVFMV MDLNKDLTAF QRGYVNQLRR FDEVERMVGF LNEVVEKHAA ETWKYILHI DDEGNDIAQP DMADLINTME PLSLENVNDM VKEITDCESR ARQLDESLDS LRSKLNDLLE QRQVIFECSK F IEVNPGIA GRATNPEIEQ EERDVDEFRM TPDDISETLS DAFSFDDETP QDRGALGNDL TRNQSVEDLS FLEQGYQHRY MI TGSIRRT KVDILNRILW RLLRGNLIFQ NFPIEEPLLE GKEKVEKDCF IIFTHGETLL KKVKRVIDSL NGKIVSLNTR SSE LVDTLN RQIDDLQRIL DTTEQTLHTE LLVIHDQLPV WSAMTKREKY VYTTLNKFQQ ESQGLIAEGW VPSTELIHLQ DSLK DYIET LGSEYSTVFN VILTNKLPPT YHRTNKFTQA FQSIVDAYGI ATYKEINAGL ATVVTFPFMF AIMFGDMGHG FILFL MALF LVLNERKFGA MHRDEIFDMA FTGRYVLLLM GAFSVYTGLL YNDIFSKSMT IFKSGWQWPS TFRKGESIEA KKTGVY PFG LDFAWHGTDN GLLFSNSYKM KLSILMGYAH MTYSFMFSYI NYRAKNSKVD IIGNFIPGLV FMQSIFGYLS WAIVYKW SK DWIKDDKPAP GLLNMLINMF LAPGTIDDQL YSGQAKLQVV LLLAALVCVP WLLLYKPLTL RRLNKNGGGG RPHGYQSV G NIEHEEQIAQ QRHSAEGFQG MIISDVASVA DSINESVGGG EQGPFNFGDV MIHQVIHTIE FCLNCISHTA SYLRLWALS LAHAQLSSVL WDMTISNAFS SKNSGSPLAV MKVVFLFAMW FVLTVCILVF MEGTSAMLHA LRLHWVEAMS KFFEGEGYAY EPFSFRAII EDYKDHDGDY KDHDIDYKDD DDK

UniProtKB: V-type proton ATPase subunit a, Golgi isoform

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Macromolecule #2: V0 assembly protein 1

MacromoleculeName: V0 assembly protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 29.694885 KDa
SequenceString: MVFGQLYALF IFTLSCCISK TVQADSSKES SSFISFDKES NWDTISTISS TADVISSVDS AIAVFEFDNF SLLDNLMIDE EYPFFNRFF ANDVSLTVHD DSPLNISQSL SPIMEQFTVD ELPESASDLL YEYSLDDKSI VLFKFTSDAY DLKKLDEFID S CLSFLEDK ...String:
MVFGQLYALF IFTLSCCISK TVQADSSKES SSFISFDKES NWDTISTISS TADVISSVDS AIAVFEFDNF SLLDNLMIDE EYPFFNRFF ANDVSLTVHD DSPLNISQSL SPIMEQFTVD ELPESASDLL YEYSLDDKSI VLFKFTSDAY DLKKLDEFID S CLSFLEDK SGDNLTVVIN SLGWAFEDED GDDEYATEET LSHHDNNKGK EGDDDILSSI WTEGLLMCLI VSALLLFILI VA LSWISNL DITYGALEKS TNPIKKNN

UniProtKB: V0 assembly protein 1

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Macromolecule #3: V-type proton ATPase subunit c''

MacromoleculeName: V-type proton ATPase subunit c'' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.610641 KDa
SequenceString: MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA ...String:
MNKESKDDDM SLGKFSFSHF LYYLVLIVVI VYGLYKLFTG HGSDINFGKF LLRTSPYMWA NLGIALCVGL SVVGAAWGIF ITGSSMIGA GVRAPRITTK NLISIIFCEV VAIYGLIIAI VFSSKLTVAT AENMYSKSNL YTGYSLFWAG ITVGASNLIC G IAVGITGA TAAISDAADS ALFVKILVIE IFGSILGLLG LIVGLLMAGK ASEFQ

UniProtKB: V-type proton ATPase subunit c''

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Macromolecule #4: V-type proton ATPase subunit d

MacromoleculeName: V-type proton ATPase subunit d / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 39.822484 KDa
SequenceString: MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT ...String:
MEGVYFNIDN GFIEGVVRGY RNGLLSNNQY INLTQCDTLE DLKLQLSSTD YGNFLSSVSS ESLTTSLIQE YASSKLYHEF NYIRDQSSG STRKFMDYIT YGYMIDNVAL MITGTIHDRD KGEILQRCHP LGWFDTLPTL SVATDLESLY ETVLVDTPLA P YFKNCFDT AEELDDMNIE IIRNKLYKAY LEDFYNFVTE EIPEPAKECM QTLLGFEADR RSINIALNSL QSSDIDPDLK SD LLPNIGK LYPLATFHLA QAQDFEGVRA ALANVYEYRG FLETGNLEDH FYQLEMELCR DAFTQQFAIS TVWAWMKSKE QEV RNITWI AECIAQNQRE RINNYISVY

UniProtKB: V-type proton ATPase subunit d

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Macromolecule #5: V-type proton ATPase subunit e

MacromoleculeName: V-type proton ATPase subunit e / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.387065 KDa
SequenceString:
MSSFYTVVGV FIVVSAMSVL FWIMAPKNNQ AVWRSTVILT LAMMFLMWAI TFLCQLHPLV APRRSDLRPE FAE

UniProtKB: V-type proton ATPase subunit e

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Macromolecule #6: Putative protein YPR170W-B

MacromoleculeName: Putative protein YPR170W-B / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.369934 KDa
SequenceString:
MRPVVSTGKA WCCTVLSAFG VVILSVIAHL FNTNHESFVG SINDPEDGPA VAHTVYLAAL VYLVFFVFCG FQVYLARRKP SIELR

UniProtKB: V-type proton ATPase subunit f

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Macromolecule #7: V-type proton ATPase subunit c

MacromoleculeName: V-type proton ATPase subunit c / type: protein_or_peptide / ID: 7 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 16.357501 KDa
SequenceString:
MTELCPVYAP FFGAIGCASA IIFTSLGAAY GTAKSGVGIC ATCVLRPDLL FKNIVPVIMA GIIAIYGLVV SVLVCYSLGQ KQALYTGFI QLGAGLSVGL SGLAAGFAIG IVGDAGVRGS SQQPRLFVGM ILILIFAEVL GLYGLIVALL LNSRATQDVV C

UniProtKB: V-type proton ATPase subunit c

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Macromolecule #8: V-type proton ATPase subunit c'

MacromoleculeName: V-type proton ATPase subunit c' / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.046361 KDa
SequenceString:
MSTQLASNIY APLYAPFFGF AGCAAAMVLS CLGAAIGTAK SGIGIAGIGT FKPELIMKSL IPVVMSGILA IYGLVVAVLI AGNLSPTED YTLFNGFMHL SCGLCVGFAC LSSGYAIGMV GDVGVRKYMH QPRLFVGIVL ILIFSEVLGL YGMIVALILN T RGSE

UniProtKB: V-type proton ATPase subunit c'

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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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 163024
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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