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- EMDB-26896: Rat Kidney V-ATPase with SidK, State 2, V1 region focused refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-26896
TitleRat Kidney V-ATPase with SidK, State 2, V1 region focused refinement
Map dataV-ATPase with SidK, State 2, V1 region focused refinement
Sample
  • Complex: Rat Kidney V-ATPase with SidK and NCOA7B
KeywordsV-ATPase / Complex / Membrane protein / PROTON TRANSPORT
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAbbas YM / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Structure of V-ATPase with NCOA7B
Authors: Abbas YM / Rubinstein JL
History
DepositionMay 9, 2022-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26896.png

Downloads & links

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Map

FileDownload / File: emd_26896.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationV-ATPase with SidK, State 2, V1 region focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 340 pix.
= 449.65 Å		1.32 Å/pix.
x 340 pix.
= 449.65 Å		1.32 Å/pix.
x 340 pix.
= 449.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3225 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.48
Minimum - Maximum-5.2785816 - 8.195337
Average (Standard dev.)0.0046290434 (±0.12871942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 449.65 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: V-ATPase with SidK, State 2, V1 region focused refinement

Fileemd_26896_half_map_1.map
AnnotationV-ATPase with SidK, State 2, V1 region focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: V-ATPase with SidK, State 2, V1 region focused refinement

Fileemd_26896_half_map_2.map
AnnotationV-ATPase with SidK, State 2, V1 region focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rat Kidney V-ATPase with SidK and NCOA7B

EntireName: Rat Kidney V-ATPase with SidK and NCOA7B
Components
  • Complex: Rat Kidney V-ATPase with SidK and NCOA7B

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Supramolecule #1: Rat Kidney V-ATPase with SidK and NCOA7B

SupramoleculeName: Rat Kidney V-ATPase with SidK and NCOA7B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 44.825 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46604
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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