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- EMDB-27985: Yeast VO missing subunits a, e, and f in complex with Vma12-22p -

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Basic information

Entry
Database: EMDB / ID: EMD-27985
TitleYeast VO missing subunits a, e, and f in complex with Vma12-22p
Map data
Sample
  • Complex: Yeast VO missing subunits a, e, and f in complex with Vma12-22p
    • Protein or peptide: Vacuolar ATPase assembly protein VMA22
    • Protein or peptide: Vacuolar ATPase assembly integral membrane protein VPH2
    • Protein or peptide: V-type proton ATPase subunit F
    • 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 c
    • Protein or peptide: V-type proton ATPase subunit c'
Function / homology
Function and homology information


Vma12-Vma22 assembly complex / extrinsic component of endoplasmic reticulum membrane / vacuolar proton-transporting V-type ATPase complex assembly / proton-transporting V-type ATPase, V1 domain / P-type proton-exporting transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification ...Vma12-Vma22 assembly complex / extrinsic component of endoplasmic reticulum membrane / vacuolar proton-transporting V-type ATPase complex assembly / proton-transporting V-type ATPase, V1 domain / P-type proton-exporting transporter activity / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / endosomal lumen acidification / protein targeting to vacuole / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuole organization / fungal-type vacuole / vacuolar acidification / fungal-type vacuole membrane / vacuolar membrane / proton transmembrane transporter activity / intracellular copper ion homeostasis / endomembrane system / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / cell periphery / endocytosis / unfolded protein binding / protein-containing complex assembly / intracellular iron ion homeostasis / membrane => GO:0016020 / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / nucleus
Similarity search - Function
ATPase, vacuolar ER assembly factor, Vma12 / Endoplasmic reticulum-based factor for assembly of V-ATPase / Vma22/CCDC115 / 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 d / V-ATPase proteolipid subunit C, eukaryotic / V-ATPase proteolipid subunit / ATPase, V0 complex, c/d subunit ...ATPase, vacuolar ER assembly factor, Vma12 / Endoplasmic reticulum-based factor for assembly of V-ATPase / Vma22/CCDC115 / 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 d / V-ATPase proteolipid subunit C, eukaryotic / V-ATPase proteolipid subunit / 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 / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / 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
V-type proton ATPase subunit F / V-type proton ATPase subunit c'' / V-type proton ATPase subunit c / Vacuolar ATPase assembly integral membrane protein VPH2 / V-type proton ATPase subunit d / V-type proton ATPase subunit c' / Vacuolar ATPase assembly protein VMA22 / V0 assembly protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang H / Bueler SA / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structural basis of V-ATPase V region assembly by Vma12p, 21p, and 22p.
Authors: Hanlin Wang / Stephanie A Bueler / John L Rubinstein /
Abstract: Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a ...Vacuolar-type adenosine triphosphatases (V-ATPases) are rotary proton pumps that acidify specific intracellular compartments in almost all eukaryotic cells. These multi-subunit enzymes consist of a soluble catalytic V region and a membrane-embedded proton-translocating V region. V is assembled in the endoplasmic reticulum (ER) membrane, and V is assembled in the cytosol. However, V binds V only after V is transported to the Golgi membrane, thereby preventing acidification of the ER. We isolated V complexes and subcomplexes from bound to V-ATPase assembly factors Vma12p, Vma21p, and Vma22p. Electron cryomicroscopy shows how the Vma12-22p complex recruits subunits a, e, and f to the rotor ring of V while blocking premature binding of V. Vma21p, which contains an ER-retrieval motif, binds the V:Vma12-22p complex, "mature" V, and a complex that appears to contain a ring of loosely packed rotor subunits and the proteins YAR027W and YAR028W. The structures suggest that Vma21p binds assembly intermediates that contain a rotor ring and that activation of proton pumping following assembly of V with V removes Vma21p, allowing V-ATPase to remain in the Golgi. Together, these structures show how Vma12-22p and Vma21p function in V-ATPase assembly and quality control, ensuring the enzyme acidifies only its intended cellular targets.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of V-ATPase V0 region assembly by Vma12p, 21p, and 22p
Authors: Wang H / Bueler SA / Rubinstein JL
History
DepositionAug 29, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27985.png

Downloads & links

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Map

FileDownload / File: emd_27985.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-4.2778206 - 7.7274637
Average (Standard dev.)0.0053639235 (±0.19376539)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27985_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27985_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast VO missing subunits a, e, and f in complex with Vma12-22p

EntireName: Yeast VO missing subunits a, e, and f in complex with Vma12-22p
Components
  • Complex: Yeast VO missing subunits a, e, and f in complex with Vma12-22p
    • Protein or peptide: Vacuolar ATPase assembly protein VMA22
    • Protein or peptide: Vacuolar ATPase assembly integral membrane protein VPH2
    • Protein or peptide: V-type proton ATPase subunit F
    • 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 c
    • Protein or peptide: V-type proton ATPase subunit c'

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Supramolecule #1: Yeast VO missing subunits a, e, and f in complex with Vma12-22p

SupramoleculeName: Yeast VO missing subunits a, e, and f in complex with Vma12-22p
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Vacuolar ATPase assembly protein VMA22

MacromoleculeName: Vacuolar ATPase assembly protein VMA22 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 21.104717 KDa
SequenceString:
MSETRMAQNM DTTDEQYLRL IELLSNYDST LEQLQKGFQD GYIQLSRSNY YNKDSLRGNY GEDYWDETYI GQLMATVEEK NSKVVVEIV KRKAQDKQEK KEEEDNKLTQ RKKGTKPEKQ KTQSHKLKQD YDPILMFGGV LSVPSSLRQS QTSFKGCIPL I AQLINYKN EILTLVETLS EQE

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Macromolecule #2: Vacuolar ATPase assembly integral membrane protein VPH2

MacromoleculeName: Vacuolar ATPase assembly integral membrane protein VPH2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 25.325648 KDa
SequenceString: MFEIKLNDRI TEFLRKFKNS AKSNEGIDED IDLFLKRHAI PMQSLLFYVK EYRKDSDLQC SIKELLKPLE FEFKPKAVRG LHYSEDFKK KLEFLKYQEQ ELEYQSMVKR SKSVFSLQED DELTPSQINK QIKEQVTTVF NVLVSVISVV VAIWYWTGSS T NFPVHVRL ...String:
MFEIKLNDRI TEFLRKFKNS AKSNEGIDED IDLFLKRHAI PMQSLLFYVK EYRKDSDLQC SIKELLKPLE FEFKPKAVRG LHYSEDFKK KLEFLKYQEQ ELEYQSMVKR SKSVFSLQED DELTPSQINK QIKEQVTTVF NVLVSVISVV VAIWYWTGSS T NFPVHVRL LLCLFFGILV LVADVVVYNS YLKKLEEAKV KEKTKVEKKK VLSKITL

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Macromolecule #3: V-type proton ATPase subunit F

MacromoleculeName: V-type proton ATPase subunit F / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (brewer's yeast)
Molecular weightTheoretical: 13.47917 KDa
SequenceString:
MAEKRTLIAV IADEDTTTGL LLAGIGQITP ETQEKNFFVY QEGKTTKEEI TDKFNHFTEE RDDIAILLIN QHIAENIRAR VDSFTNAFP AILEIPSKDH PYDPEKDSVL KRVRKLFGE

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Macromolecule #4: V0 assembly protein 1

MacromoleculeName: V0 assembly protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (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

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Macromolecule #5: V-type proton ATPase subunit c''

MacromoleculeName: V-type proton ATPase subunit c'' / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (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

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Macromolecule #6: V-type proton ATPase subunit d

MacromoleculeName: V-type proton ATPase subunit d / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: baker's yeast (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

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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: baker's yeast (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

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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: baker's yeast (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

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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
GridModel: Homemade / Material: COPPER/RHODIUM
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114346
FSC plot (resolution estimation)

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