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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
Citation
Journal: Cell Death Differ / Year: 2026
Title: A planar dimer of bovine ATP synthase.
Authors: Chimari Jiko / Atsuki Nakano / Yosuke Teshirogi / Eiki Yamashita / Genji Kurisu / Daron Standley / Tohru Terada / Kaoru Mitsuoka / Ken Yokoyama / Christoph Gerle /
Abstract: Mammalian mitochondrial ATP synthase typically organizes into rows of V-shaped dimers that impose significant membrane curvature essential for mitochondrial cristae formation. Using gentle, column- ...Mammalian mitochondrial ATP synthase typically organizes into rows of V-shaped dimers that impose significant membrane curvature essential for mitochondrial cristae formation. Using gentle, column-free purification combined with single-particle cryo-electron microscopy, we have identified a previously unrecognized planar dimeric form of bovine ATP synthase exhibiting minimal membrane bending. This planar dimer is characterized structurally by anti-parallel arrangement of two ATP synthase complexes linked by a straight conformation of inhibitory factor 1 (IF1), a sharp contrast to the kinked IF1 observed in tetrameric assemblies. Molecular dynamics simulations confirm that transitioning between straight and kinked IF1 conformations occurs without significant energetic barriers. The planar dimer also displays distinct peripheral stalk positioning relative to its adjacent α subunit. These structural divergences suggest a specialized function and a distinct localization for planar ATP synthase dimers, providing structural support for a division of labor within mitochondrial ATP synthase populations.
#1: Journal: 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 15, 2026-
Current statusJul 15, 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
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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)

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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

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Half map: half map A

Fileemd_65245_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Histogram

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Half map: half map B

Fileemd_65245_half_map_2.map
Annotationhalf map B
Projections & Slices
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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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