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- EMDB-46463: Consensus map of yeast RAVE bound to V-ATPase V1 -

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Basic information

Entry
Database: EMDB / ID: EMD-46463
TitleConsensus map of yeast RAVE bound to V-ATPase V1
Map data
Sample
  • Complex: Yeast RAVE bound to V-ATPase V1 complex
KeywordsV-ATPase / RAVE / assembly / HYDROLASE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang H / Rubinstein JL
Funding support United States, Canada, 2 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1R35GM145256 United States
Canadian Institutes of Health Research (CIHR)PJT166152 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure of yeast RAVE bound to a partial V complex.
Authors: Hanlin Wang / Maureen Tarsio / Patricia M Kane / John L Rubinstein /
Abstract: Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multisubunit enzymes ...Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multisubunit enzymes consist of a soluble catalytic V subcomplex and a membrane-embedded proton-translocating V subcomplex. The V and V subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V and V requiring the protein complex known as RAVE (regulator of the ATPase of vacuoles and endosomes). In the yeast , RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V. In the structure, RAVE is an L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V. Only Rav1p interacts with V, binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V is in a rotational state suitable for binding the free V complex, but in the structure, it is partially disrupted, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V complex with RAVE appears poised for reassembly with V.
History
DepositionAug 7, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46463.png

Downloads & links

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Map

FileDownload / File: emd_46463.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 390 pix.
= 401.7 Å		1.03 Å/pix.
x 390 pix.
= 401.7 Å		1.03 Å/pix.
x 390 pix.
= 401.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.3815313 - 2.2775416
Average (Standard dev.)0.0075854524 (±0.045463234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions390390390
Spacing390390390
CellA=B=C: 401.69998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_46463_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_46463_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast RAVE bound to V-ATPase V1 complex

EntireName: Yeast RAVE bound to V-ATPase V1 complex
Components
  • Complex: Yeast RAVE bound to V-ATPase V1 complex

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Supramolecule #1: Yeast RAVE bound to V-ATPase V1 complex

SupramoleculeName: Yeast RAVE bound to V-ATPase V1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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 / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71341
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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