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- EMDB-49663: Porcine ATP synthase with inhibitory protein IF1, F1 domain, DP-state -

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Basic information

Entry
Database: EMDB / ID: EMD-49663
TitlePorcine ATP synthase with inhibitory protein IF1, F1 domain, DP-state
Map dataPorcine ATP synthase with inhibitory protein IF1, F1 domain, DP-state
Sample
  • Complex: Mitochondrial ATP synthase
KeywordsATP synthesis / Complex V / mitochondria / oxidative-phosphorylation / MEMBRANE PROTEIN
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsMnatsakanyan N / Mello JFR / Palles C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG072484 United States
CitationJournal: To Be Published
Title: ATP synthase with inhibitory protein IF1, F1 domain, DP-state
Authors: Mnatsakanyan N / Mello JFR / Palles C
History
DepositionMar 12, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49663.png

Downloads & links

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Map

FileDownload / File: emd_49663.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPorcine ATP synthase with inhibitory protein IF1, F1 domain, DP-state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 546.816 Å		1.07 Å/pix.
x 512 pix.
= 546.816 Å		1.07 Å/pix.
x 512 pix.
= 546.816 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.5273252 - 4.632051
Average (Standard dev.)-0.0015982655 (±0.102002844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 546.816 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_49663_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49663_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial ATP synthase

EntireName: Mitochondrial ATP synthase
Components
  • Complex: Mitochondrial ATP synthase

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Supramolecule #1: Mitochondrial ATP synthase

SupramoleculeName: Mitochondrial ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 700 KDa

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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

Concentration0.5 mg/mL
BufferpH: 7.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 15.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105447
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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