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- EMDB-20323: Yeast Vo motor in complex with 2 VopQ molecules -

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Basic information

Entry
Database: EMDB / ID: EMD-20323
TitleYeast Vo motor in complex with 2 VopQ molecules
Map dataem-volume_P1
Sample
  • Complex: Yeast Vo motor in complex with 2 VopQ molecules
    • Protein or peptide: V-type proton ATPase subunit a, vacuolar isoform
    • Protein or peptide: V0 assembly protein 1
    • Protein or peptide: V-type proton ATPase subunit d
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: Uncharacterized protein YPR170W-B
    • Protein or peptide: V-type proton ATPase subunit c''
    • Protein or peptide: V-type proton ATPase subunit c'
    • Protein or peptide: V-type proton ATPase subunit c
    • Protein or peptide: Cation transporter
Keywordscomplex / TRANSPORT PROTEIN
Function / homology
Function and homology information


cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification ...cell wall mannoprotein biosynthetic process / ATPase-coupled ion transmembrane transporter activity / protein localization to vacuolar membrane / cellular response to alkaline pH / polyphosphate metabolic process / 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 / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / vacuole organization / protein targeting to vacuole / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / fungal-type vacuole / cellular hyperosmotic response / vacuolar acidification / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton transmembrane transporter activity / intracellular copper ion homeostasis / proton-transporting ATPase activity, rotational mechanism / Neutrophil degranulation / RNA endonuclease activity / proton transmembrane transport / cell periphery / transmembrane transport / endocytosis / ATPase binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane raft / Golgi membrane / endoplasmic reticulum membrane / membrane
Similarity search - Function
: / 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, 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 ...: / 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, 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
: / Cation transporter / 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 a, vacuolar isoform / V-type proton ATPase subunit c' / V0 assembly protein 1 / V-type proton ATPase subunit e
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Vibrio parahaemolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPeng W / Li Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Welch Foundation United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM.
Authors: Wei Peng / Amanda K Casey / Jessie Fernandez / Emily M Carpinone / Kelly A Servage / Zhe Chen / Yang Li / Diana R Tomchick / Vincent J Starai / Kim Orth /
Abstract: The Vibrio parahaemolyticus T3SS effector VopQ targets host-cell V-ATPase, resulting in blockage of autophagic flux and neutralization of acidic compartments. Here, we report the cryo-EM structure of ...The Vibrio parahaemolyticus T3SS effector VopQ targets host-cell V-ATPase, resulting in blockage of autophagic flux and neutralization of acidic compartments. Here, we report the cryo-EM structure of VopQ bound to the V subcomplex of the V-ATPase. VopQ inserts into membranes and forms an unconventional pore while binding directly to subunit c of the V-ATPase membrane-embedded subcomplex V. We show that VopQ arrests yeast growth in vivo by targeting the immature V subcomplex in the endoplasmic reticulum (ER), thus providing insight into the observation that VopQ kills cells in the absence of a functional V-ATPase. VopQ is a bacterial effector that has been discovered to inhibit a host-membrane megadalton complex by coincidentally binding its target, inserting into a membrane and disrupting membrane potential. Collectively, our results reveal a mechanism by which bacterial effectors modulate host cell biology and provide an invaluable tool for future studies on V-ATPase-mediated membrane fusion and autophagy.
History
DepositionJun 20, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseMay 20, 2020-
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: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pe5
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20323.png

Downloads & links

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Map

FileDownload / File: emd_20323.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationem-volume_P1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.080374226 - 0.14256164
Average (Standard dev.)0.0001935283 (±0.0060505997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z299.600299.600299.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0800.1430.000

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Supplemental data

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Sample components

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Entire : Yeast Vo motor in complex with 2 VopQ molecules

EntireName: Yeast Vo motor in complex with 2 VopQ molecules
Components
  • Complex: Yeast Vo motor in complex with 2 VopQ molecules
    • Protein or peptide: V-type proton ATPase subunit a, vacuolar isoform
    • Protein or peptide: V0 assembly protein 1
    • Protein or peptide: V-type proton ATPase subunit d
    • Protein or peptide: V-type proton ATPase subunit e
    • Protein or peptide: Uncharacterized protein YPR170W-B
    • Protein or peptide: V-type proton ATPase subunit c''
    • Protein or peptide: V-type proton ATPase subunit c'
    • Protein or peptide: V-type proton ATPase subunit c
    • Protein or peptide: Cation transporter

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Supramolecule #1: Yeast Vo motor in complex with 2 VopQ molecules

SupramoleculeName: Yeast Vo motor in complex with 2 VopQ molecules / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 460 KDa

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

MacromoleculeName: V-type proton ATPase subunit a, vacuolar isoform / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 115.126023 KDa
SequenceString: MAEKEEAIFR SAEMALVQFY IPQEISRDSA YTLGQLGLVQ FRDLNSKVRA FQRTFVNEIR RLDNVERQYR YFYSLLKKHD IKLYEGDTD KYLDGSGELY VPPSGSVIDD YVRNASYLEE RLIQMEDATD QIEVQKNDLE QYRFILQSGD EFFLKGDNTD S TSYMDEDM ...String:
MAEKEEAIFR SAEMALVQFY IPQEISRDSA YTLGQLGLVQ FRDLNSKVRA FQRTFVNEIR RLDNVERQYR YFYSLLKKHD IKLYEGDTD KYLDGSGELY VPPSGSVIDD YVRNASYLEE RLIQMEDATD QIEVQKNDLE QYRFILQSGD EFFLKGDNTD S TSYMDEDM IDANGENIAA AIGASVNYVT GVIARDKVAT LEQILWRVLR GNLFFKTVEI EQPVYDVKTR EYKHKNAFIV FS HGDLIIK RIRKIAESLD ANLYDVDSSN EGRSQQLAKV NKNLSDLYTV LKTTSTTLES ELYAIAKELD SWFQDVTREK AIF EILNKS NYDTNRKILI AEGWIPRDEL ATLQARLGEM IARLGIDVPS IIQVLDTNHT PPTFHRTNKF TAGFQSICDC YGIA QYREI NAGLPTIVTF PFMFAIMFGD MGHGFLMTLA ALSLVLNEKK INKMKRGEIF DMAFTGRYII LLMGVFSMYT GFLYN DIFS KTMTIFKSGW KWPDHWKKGE SITATSVGTY PIGLDWAWHG TENALLFSNS YKMKLSILMG FIHMTYSYFF SLANHL YFN SMIDIIGNFI PGLLFMQGIF GYLSVCIVYK WAVDWVKDGK PAPGLLNMLI NMFLSPGTID DELYPHQAKV QVFLLLM AL VCIPWLLLVK PLHFKFTHKK KSHEPLPSTE ADASSEDLEA QQLISAMDAD DAEEEEVGSG SHGEDFGDIM IHQVIHTI E FCLNCVSHTA SYLRLWALSL AHAQLSSVLW TMTIQIAFGF RGFVGVFMTV ALFAMWFALT CAVLVLMEGT SAMLHSLRL HWVESMSKFF VGEGLPYEPF AFEYKDMEVA VASASSSASS SMEKRRWKKN FIAVSAANRF KKISSSGALD YDIPTTASEN LYFQGELKT AALAQHDEAV DNFNKEQQNA FYEILHLPNL NEEQRNAFIQ SLKDDPSQSA NLLAEAKKLN DAQAPKVDNF N KEQQNAFY EILHLPNLNE EQRNAFIQSL KDDPSQSANL LAEAKKLNDA QAPK

UniProtKB: V-type proton ATPase subunit a, vacuolar 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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 d

MacromoleculeName: V-type proton ATPase subunit d / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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 #4: V-type proton ATPase subunit e

MacromoleculeName: V-type proton ATPase subunit e / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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 #5: Uncharacterized protein YPR170W-B

MacromoleculeName: Uncharacterized protein YPR170W-B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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 #6: V-type proton ATPase subunit c''

MacromoleculeName: V-type proton ATPase subunit c'' / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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 #7: V-type proton ATPase subunit c'

MacromoleculeName: V-type proton ATPase subunit c' / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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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Macromolecule #8: V-type proton ATPase subunit c

MacromoleculeName: V-type proton ATPase subunit c / type: protein_or_peptide / ID: 8 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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 #9: Cation transporter

MacromoleculeName: Cation transporter / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio parahaemolyticus (bacteria)
Molecular weightTheoretical: 55.424668 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDLDEVDAG SMVNTTQKIS QSPVPDLEQF RAIAAQKDDR VISKRGEVKE PSTFHKGHKF ASVSEGVLRK KYTKFFQEN IKTHLDLKQA LLKEEKPETA LLAYSLVSPS GYRGEPLTER KILEVVSLLD EVKVDGDTYQ QLKNTFDSIS K DPRMQVSL ...String:
MGSSHHHHHH SQDLDEVDAG SMVNTTQKIS QSPVPDLEQF RAIAAQKDDR VISKRGEVKE PSTFHKGHKF ASVSEGVLRK KYTKFFQEN IKTHLDLKQA LLKEEKPETA LLAYSLVSPS GYRGEPLTER KILEVVSLLD EVKVDGDTYQ QLKNTFDSIS K DPRMQVSL ENQYPGKMDG FGAQLLEMGK EKLKGSGVNA AINLALPGVG LLVATGRELH KASVNGDAEA YHHQLEQISQ LP GRDQRLS MPMQQTLAIG HAMLSAEGAV GATLGMATGG LGTFGVSSVA TAGVTPIAKE AIGTALTTGI ISGGGFVAGQ AGA YGLNNE VQDQLKQGPM SGVLPRLEIS NVKGDFTFSM QEPAAVRALM AYLGPKEDTS MSSPQAPKEA QEMEAARLTL KQML GSSPN EHLVPDVDSL LKLSDEDMPS QTESTANGAF KKLLSEDWDW LMPAVRAMDK GEAGKINEKL TYKLPLDAAN GRVYL DKSP NLSDAQLDAL DKLGSPSQLR LMYLAEGWI

UniProtKB: UNIPROTKB: A0A0L7YPA6

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72837
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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