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- EMDB-65587: Cryo-EM structure of complex IV on the bovine heart submitochondr... -

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Entry
Database: EMDB / ID: EMD-65587
TitleCryo-EM structure of complex IV on the bovine heart submitochondrial particles, IV-C
Map data
Sample
  • Complex: Complex IV on the bovine heart submitochondrial particles
Keywordsrespiratory chain complex / supercomplex / submitochondrial particles / OXIDOREDUCTASE
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsNakano A / Masuya T / Akisada S / Ishikawa-Fukuda M / Mitsuoka K / Miyoshi H / Murai M / Yokoyama K
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
Japan Society for the Promotion of Science (JSPS)25K01958 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Nat Commun / Year: 2026
Title: Structures of respiratory supercomplexes and ATP synthase oligomers in mammalian mitochondrial inner membrane.
Authors: Atsuki Nakano / Takahiro Masuya / Shinsuke Akisada / Moe Ishikawa-Fukuda / Kaoru Mitsuoka / Hideto Miyoshi / Masatoshi Murai / Ken Yokoyama /
Abstract: Understanding the functional mechanisms of membrane protein complexes requires structural analysis within their native membrane environment. Here, we applied cryo-electron microscopy to determine the ...Understanding the functional mechanisms of membrane protein complexes requires structural analysis within their native membrane environment. Here, we applied cryo-electron microscopy to determine the structures of FF ATP synthase and respiratory supercomplexes (SCs) on sub-mitochondrial particles (SMPs) isolated from bovine heart mitochondria. Most FF complexes were observed as dimers stabilized by the regulatory factor IF₁, and a tetrameric assembly comprising two FF-IF₁ dimers arranged linearly was also identified. This finding indicates that the tetrameric units of FF are present in the mitochondrial inner membrane and contribute to shaping cristae tips in mammalian mitochondria. F domain maps resolve the e-subunit- c₈-ring interface and show no discrete density for a tightly bound lipid within the c₈-ring. In addition to the previously reported SCs compositions CI₁CIII₂CIV₁ and CI₁CIII₂CIV₂, our analysis identified an additional assembly with the composition CI₁CIII₂CIV₃, as well as a CI₂CIII₂CIV₆ mega-complex. This approach enables rapid structural determination of FF ATP synthase and SCs from minimal membrane fractions, providing a foundation for elucidating the molecular basis of metabolic disorders and mitochondrial diseases at the level of higher-order architecture.
History
DepositionJul 28, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65587.png

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Map

FileDownload / File: emd_65587.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 600 pix.
= 654. Å		1.09 Å/pix.
x 600 pix.
= 654. Å		1.09 Å/pix.
x 600 pix.
= 654. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
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Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.48236167 - 1.0274363
Average (Standard dev.)0.00023873862 (±0.012839115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 654.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65587_msk_1.map
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Additional map: #1

Fileemd_65587_additional_1.map
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Half map: #1

Fileemd_65587_half_map_1.map
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Half map: #2

Fileemd_65587_half_map_2.map
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Sample components

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Entire : Complex IV on the bovine heart submitochondrial particles

EntireName: Complex IV on the bovine heart submitochondrial particles
Components
  • Complex: Complex IV on the bovine heart submitochondrial particles

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Supramolecule #1: Complex IV on the bovine heart submitochondrial particles

SupramoleculeName: Complex IV on the bovine heart submitochondrial particles
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 200 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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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: 1.8 µm / Nominal defocus min: 0.8 µm
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: INSILICO MODEL
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 26116
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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