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- EMDB-26824: Citrus V-ATPase State 1, Highest-Resolution Class -

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Basic information

Entry
Database: EMDB / ID: EMD-26824
TitleCitrus V-ATPase State 1, Highest-Resolution Class
Map dataCitrus V-ATPase State 1, Highest-Resolution Class
Sample
  • Complex: Citrus V-ATPase
KeywordsV-ATPase / rotary ATPase / complex / MEMBRANE PROTEIN
Biological speciesCitrus limon (lemon)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsTan YZ / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Structure / Year: 2022
Title: Structure of V-ATPase from citrus fruit.
Authors: Yong Zi Tan / Kristine A Keon / Rana Abdelaziz / Peter Imming / Waltraud Schulze / Karin Schumacher / John L Rubinstein /
Abstract: We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, ...We used the Legionella pneumophila effector SidK to affinity purify the endogenous vacuolar-type ATPases (V-ATPases) from lemon fruit. The preparation was sufficient for cryoelectron microscopy, allowing structure determination of the enzyme in two rotational states. The structure defines the ATP:H ratio of the enzyme, demonstrating that it can establish a maximum ΔpH of ∼3, which is insufficient to maintain the low pH observed in the vacuoles of juice sac cells in lemons and other citrus fruit. Compared with yeast and mammalian enzymes, the membrane region of the plant V-ATPase lacks subunit f and possesses an unusual configuration of transmembrane α helices. Subunit H, which inhibits ATP hydrolysis in the isolated catalytic region of V-ATPase, adopts two different conformations in the intact complex, hinting at a role in modulating activity in the intact enzyme.
History
DepositionMay 3, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26824.png

Downloads & links

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Map

FileDownload / File: emd_26824.map.gz / Format: CCP4 / Size: 15 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCitrus V-ATPase State 1, Highest-Resolution Class
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 200 pix.
= 323.4 Å		1.62 Å/pix.
x 140 pix.
= 226.38 Å		1.62 Å/pix.
x 140 pix.
= 226.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.617 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-0.516186 - 4.9339457
Average (Standard dev.)0.136728 (±0.28559712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin808051
Dimensions140140200
Spacing140140200
CellA: 226.38 Å / B: 226.38 Å / C: 323.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Citrus V-ATPase State 1, Highest-Resolution Class

Fileemd_26824_additional_1.map
AnnotationCitrus V-ATPase State 1, Highest-Resolution Class
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Citrus V-ATPase State 1, Highest-Resolution Class

Fileemd_26824_half_map_1.map
AnnotationCitrus V-ATPase State 1, Highest-Resolution Class
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Citrus V-ATPase State 1, Highest-Resolution Class

Fileemd_26824_half_map_2.map
AnnotationCitrus V-ATPase State 1, Highest-Resolution Class
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Citrus V-ATPase

EntireName: Citrus V-ATPase
Components
  • Complex: Citrus V-ATPase

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Supramolecule #1: Citrus V-ATPase

SupramoleculeName: Citrus V-ATPase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Citrus limon (lemon)

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 31.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.414211 µm / Nominal defocus min: 0.677558 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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 189756
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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