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- EMDB-48490: Reconstituted yeast V-ATPase bound to Rtc5p - C (focused) -

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Basic information

Entry
Database: EMDB / ID: EMD-48490
TitleReconstituted yeast V-ATPase bound to Rtc5p - C (focused)
Map dataV1Vo_Rtc5recon_C_main
Sample
  • Complex: Reconstituted yeast V-ATPase bound to Rtc5p
KeywordsVacuolar ATPase / proton pump / Rtc5p / membrane protein / HYDROLASE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.33 Å
AuthorsWilkens S / Khan MM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141908 United States
CitationJournal: To Be Published
Title: TLDc Protein Rtc5p Assembles Yeast V-ATPase
Authors: Wilkens S / Khan MM
History
DepositionDec 28, 2024-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48490.png

Downloads & links

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Map

FileDownload / File: emd_48490.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationV1Vo_Rtc5recon_C_main
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.016266832 - 0.03807028
Average (Standard dev.)-0.00008075699 (±0.0004770836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48490_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: V1Vo Rtc5recon C half1

Fileemd_48490_half_map_1.map
AnnotationV1Vo_Rtc5recon_C_half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: V1Vo Rtc5recon C half2

Fileemd_48490_half_map_2.map
AnnotationV1Vo_Rtc5recon_C_half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Reconstituted yeast V-ATPase bound to Rtc5p

EntireName: Reconstituted yeast V-ATPase bound to Rtc5p
Components
  • Complex: Reconstituted yeast V-ATPase bound to Rtc5p

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Supramolecule #1: Reconstituted yeast V-ATPase bound to Rtc5p

SupramoleculeName: Reconstituted yeast V-ATPase bound to Rtc5p / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.1 MDa

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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

Concentration2 mg/mL
BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 279 K / Instrument: LEICA EM GP / Details: Leica EM GP2.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 7819 / Average exposure time: 5.82 sec. / Average electron dose: 52.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 92000

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Image processing

Particle selectionNumber selected: 332570
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 90977
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7fda

source_name: PDB, initial_model_type: experimental model
chain_id: R, source_name: AlphaFold, initial_model_type: in silico model
SoftwareName: Coot

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