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- EMDB-65245: IF1 bound bovine ATP synthase monomer: rotary state 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-65245
TitleIF1 bound bovine ATP synthase monomer: rotary state 3
Map dataIF1 bound bovine ATP synthase monomer: rotary state 3
Sample
  • Complex: IF1 bound bovine ATP synthase monomer: rotary state 3
KeywordsATP synthase/hydrolase / oligomer / membrane bending / mammalian mitochondria / membrane protein / motor protein
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsNakano A / Jiko C / Yamashita E / Yokoyama K / Gerle C
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
CitationJournal: Biorxiv / Year: 2025
Title: A planar dimer of bovine ATP synthase
Authors: Jiko C / Nakano A / Teshirogi Y / Yamashita E / Kurisu G / Standley D / Terada T / Mitsuoka K / Yokoyama K / Gerle C
History
DepositionJul 3, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65245.png

Downloads & links

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Map

FileDownload / File: emd_65245.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIF1 bound bovine ATP synthase monomer: rotary state 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 340 pix.
= 319.199 Å		0.94 Å/pix.
x 340 pix.
= 319.199 Å		0.94 Å/pix.
x 340 pix.
= 319.199 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93882 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.39434773 - 1.1333075
Average (Standard dev.)0.00049808255 (±0.030690666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 319.1988 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65245_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_65245_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_65245_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : IF1 bound bovine ATP synthase monomer: rotary state 3

EntireName: IF1 bound bovine ATP synthase monomer: rotary state 3
Components
  • Complex: IF1 bound bovine ATP synthase monomer: rotary state 3

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Supramolecule #1: IF1 bound bovine ATP synthase monomer: rotary state 3

SupramoleculeName: IF1 bound bovine ATP synthase monomer: rotary state 3 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 600 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

Concentration5 mg/mL
BufferpH: 7.3
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 488235
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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