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- EMDB-8070: Yeast V-ATPase average of densities, a subunit segment -

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Basic information

Entry
Database: EMDB / ID: EMD-8070
TitleYeast V-ATPase average of densities, a subunit segment
Map dataNone
Sample
  • Complex: V-ATPase
    • Complex: V-ATPase a subunit
      • Protein or peptide: V-type proton ATPase subunit a, vacuolar isoform
KeywordsV-ATPase / Vo region / membrane protein
Function / homology
Function and homology information


cellular response to alkaline pH / protein localization to vacuolar membrane / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / fungal-type vacuole / vacuolar proton-transporting V-type ATPase complex ...cellular response to alkaline pH / protein localization to vacuolar membrane / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / fungal-type vacuole / vacuolar proton-transporting V-type ATPase complex / cellular hyperosmotic response / vacuolar acidification / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / proton-transporting ATPase activity, rotational mechanism / Neutrophil degranulation / proton transmembrane transport / ATPase binding / protein-containing complex assembly / membrane raft
Similarity search - Function
ATPase, V0 complex, subunit 116kDa, eukaryotic / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family
Similarity search - Domain/homology
V-type proton ATPase subunit a, vacuolar isoform
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsSchep DG / Zhao J
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 81294 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance.
Authors: Daniel G Schep / Jianhua Zhao / John L Rubinstein /
Abstract: Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the ...Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases.
History
DepositionFeb 5, 2016-
Header (metadata) releaseMar 9, 2016-
Map releaseMar 9, 2016-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5i1m
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5i1m
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5i1m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8070.png

Downloads & links

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Map

FileDownload / File: emd_8070.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 320 pix.
= 464. Å		1.45 Å/pix.
x 320 pix.
= 464. Å		1.45 Å/pix.
x 320 pix.
= 464. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.0059027663 - 0.03360682
Average (Standard dev.)0.00010624225 (±0.0025233699)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 464.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z464.000464.000464.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ129141209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0060.0340.000

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Supplemental data

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Additional map: None

Fileemd_8070_additional.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : V-ATPase

EntireName: V-ATPase
Components
  • Complex: V-ATPase
    • Complex: V-ATPase a subunit
      • Protein or peptide: V-type proton ATPase subunit a, vacuolar isoform

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Supramolecule #1: V-ATPase

SupramoleculeName: V-ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Six maps of the V-ATPase, averaged with the Vo regions aligned
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: JTY2

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Supramolecule #2: V-ATPase a subunit

SupramoleculeName: V-ATPase a subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Details: Segment of averaged densities from six maps of the V-ATPase, aligned to the a subunit. This does not contain the c ring or micelle, but has some densities that are not assigned to the a ...Details: Segment of averaged densities from six maps of the V-ATPase, aligned to the a subunit. This does not contain the c ring or micelle, but has some densities that are not assigned to the a subunit and likely represent unknown subunits.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: JTY2

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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 (brewer's yeast) / Strain: JTY2
Molecular weightTheoretical: 51.548867 KDa
SequenceString: TNKFTAGFQS ICDCYGIAQY REINAGLPTI VTFPFMFAIM FGDMGHGFLM TLAALSLVLN EKKINKMKRG EIFDMAFTGR YIILLMGVF SMYTGFLYND IFSKTMTIFK SGWKWPDHWK KGESITATSV GTYPIGLDWA WHGTENALLF SNSYKMKLSI L MGFIHMTY ...String:
TNKFTAGFQS ICDCYGIAQY REINAGLPTI VTFPFMFAIM FGDMGHGFLM TLAALSLVLN EKKINKMKRG EIFDMAFTGR YIILLMGVF SMYTGFLYND IFSKTMTIFK SGWKWPDHWK KGESITATSV GTYPIGLDWA WHGTENALLF SNSYKMKLSI L MGFIHMTY SYFFSLANHL YFNSMIDIIG NFIPGLLFMQ GIFGYLSVCI VYKWAVDWVK DGKPAPGLLN MLINMFLSPG TI DDELYPH QAKVQVFLLL MALVCIPWLL LVKPLHFKFT HKKKSHEPLP STEADASSED LEAQQLISAM DADDAEEEEV GSG SHGEDF GDIMIHQVIH TIEFCLNCVS HTASYLRLWA LSLAHAQLSS VLWTMTIQIA FGFRGFVGVF MTVALFAMWF ALTC AVLVL MEGTSAMLHS LRLHWVESMS KFFVGEGLPY EPFAFEYKDM EVAVASASSS ASS

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

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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 TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 35.7 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: OTHER
Details: Resolution is approximated from the resolutions of the aligned and averaged maps that yielded the density.
Number images used: 269377
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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