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- EMDB-34145: E. hirae V-ATPase state 1 (V1 domain) -

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Basic information

Entry
Database: EMDB / ID: EMD-34145
TitleE. hirae V-ATPase state 1 (V1 domain)
Map dataEhVATPase S1 V1
Sample
  • Complex: E. hirae V-ATPase state 1 (V1 domain)
KeywordsSodium transport / V-ATPase / Membrane complex / MEMBRANE PROTEIN
Biological speciesEnterococcus hirae ATCC 9790 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBurton Smith RN / Murata K
Funding support Japan, 5 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H06280 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19H05380 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP18H05425 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP18H05424 Japan
CitationJournal: Commun Biol / Year: 2023
Title: Six states of Enterococcus hirae V-type ATPase reveals non-uniform rotor rotation during turnover.
Authors: Raymond N Burton-Smith / Chihong Song / Hiroshi Ueno / Takeshi Murata / Ryota Iino / Kazuyoshi Murata /
Abstract: The vacuolar-type ATPase from Enterococcus hirae (EhV-ATPase) is a thus-far unique adaptation of V-ATPases, as it performs Na transport and demonstrates an off-axis rotor assembly. Recent single ...The vacuolar-type ATPase from Enterococcus hirae (EhV-ATPase) is a thus-far unique adaptation of V-ATPases, as it performs Na transport and demonstrates an off-axis rotor assembly. Recent single molecule studies of the isolated V domain have indicated that there are subpauses within the three major states of the pseudo three-fold symmetric rotary enzyme. However, there was no structural evidence for these. Herein we activate the EhV-ATPase complex with ATP and identified multiple structures consisting of a total of six states of this complex by using cryo-electron microscopy. The orientations of the rotor complex during turnover, especially in the intermediates, are not as perfectly uniform as expected. The densities in the nucleotide binding pockets in the V domain indicate the different catalytic conditions for the six conformations. The off-axis rotor and its' interactions with the stator a-subunit during rotation suggests that this non-uniform rotor rotation is performed through the entire complex.
History
DepositionAug 22, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34145.png

Downloads & links

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Map

FileDownload / File: emd_34145.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEhVATPase S1 V1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 360 pix.
= 363.6 Å		1.01 Å/pix.
x 360 pix.
= 363.6 Å		1.01 Å/pix.
x 360 pix.
= 363.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.025441477 - 0.046172727
Average (Standard dev.)0.000078554396 (±0.0010383277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 363.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EhVATPase S1 V1 half map 1

Fileemd_34145_half_map_1.map
AnnotationEhVATPase S1 V1 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EhVATPase S1 V1 half map 2

Fileemd_34145_half_map_2.map
AnnotationEhVATPase S1 V1 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. hirae V-ATPase state 1 (V1 domain)

EntireName: E. hirae V-ATPase state 1 (V1 domain)
Components
  • Complex: E. hirae V-ATPase state 1 (V1 domain)

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Supramolecule #1: E. hirae V-ATPase state 1 (V1 domain)

SupramoleculeName: E. hirae V-ATPase state 1 (V1 domain) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Enterococcus hirae ATCC 9790 (bacteria)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 185127
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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