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- EMDB-32034: Structure of unmodified E. hirae V-type ATPase using Volta phase plate -

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Basic information

Entry
Database: EMDB / ID: EMD-32034
TitleStructure of unmodified E. hirae V-type ATPase using Volta phase plate
Map dataE. hirae V-ATPase (native type)
Sample
  • Complex: Recombinant, unmodified E. hirae V-ATPase by Volta phase plate
Biological speciesEnterococcus hirae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsBurton-Smith RN / Murata K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: To Be Published
Title: Examining E. hirae V-ATPase by Zernike and Volta phase plate cryo-EM
Authors: Burton-Smith RN / Murata K
History
DepositionOct 8, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateOct 12, 2022-
Current statusOct 12, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32034.png

Downloads & links

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Map

FileDownload / File: emd_32034.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. hirae V-ATPase (native type)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 320 pix.
= 356.16 Å		1.11 Å/pix.
x 320 pix.
= 356.16 Å		1.11 Å/pix.
x 320 pix.
= 356.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.113 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027
Minimum - Maximum-0.012557508 - 0.055230442
Average (Standard dev.)7.690716e-05 (±0.005007727)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 356.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Recombinant, unmodified E. hirae V-ATPase by Volta phase plate

EntireName: Recombinant, unmodified E. hirae V-ATPase by Volta phase plate
Components
  • Complex: Recombinant, unmodified E. hirae V-ATPase by Volta phase plate

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Supramolecule #1: Recombinant, unmodified E. hirae V-ATPase by Volta phase plate

SupramoleculeName: Recombinant, unmodified E. hirae V-ATPase by Volta phase plate
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Enterococcus hirae (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: FEI FALCON III (4k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73711
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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