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- EMDB-26904: Rat Kidney V1 Complex with SidK and NCOA7B, State 1, Subunit EGAB... -

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Basic information

Entry
Database: EMDB / ID: EMD-26904
TitleRat Kidney V1 Complex with SidK and NCOA7B, State 1, Subunit EGABC and NCOA7B focused refinement
Map dataV1 Complex with SidK and NCOA7B, State 1, Subunit EGABC and NCOA7B focused refinement
Sample
  • Complex: Rat Kidney V1 with SidK and NCOA7B
KeywordsV-ATPase / Complex / Membrane protein / PROTON TRANSPORT
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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_26904.png

Downloads & links

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Map

FileDownload / File: emd_26904.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationV1 Complex with SidK and NCOA7B, State 1, Subunit EGABC and NCOA7B focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 350 pix.
= 371. Å		1.06 Å/pix.
x 350 pix.
= 371. Å		1.06 Å/pix.
x 350 pix.
= 371. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.63
Minimum - Maximum-5.9572654 - 8.433263
Average (Standard dev.)0.001411613 (±0.07514764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 370.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: V1 Complex with SidK and NCOA7B, State 1,...

Fileemd_26904_half_map_1.map
AnnotationV1 Complex with SidK and NCOA7B, State 1, Subunit EGABC and NCOA7B focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: V1 Complex with SidK and NCOA7B, State 1,...

Fileemd_26904_half_map_2.map
AnnotationV1 Complex with SidK and NCOA7B, State 1, Subunit EGABC and NCOA7B 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 V1 with SidK and NCOA7B

EntireName: Rat Kidney V1 with SidK and NCOA7B
Components
  • Complex: Rat Kidney V1 with SidK and NCOA7B

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Supramolecule #1: Rat Kidney V1 with SidK and NCOA7B

SupramoleculeName: Rat Kidney V1 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: 40.826 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: 0.3 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46258
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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