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- EMDB-65579: Cryo-EM structure of Fo domain of FoF1-ATPase monomer state on th... -

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Basic information

Entry
Database: EMDB / ID: EMD-65579
TitleCryo-EM structure of Fo domain of FoF1-ATPase monomer state on the bovine heart submitochondrial particles
Map data
Sample
  • Complex: FoF1-ATPase on the bovine heart submitochondrial particles
    • Protein or peptide: ATP synthase F(0) complex subunit 8
    • Protein or peptide: ATP synthase F(0) complex subunit C1, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit a
    • Protein or peptide: ATP synthase peripheral stalk subunit b, mitochondrial
    • Protein or peptide: ATP synthase peripheral stalk subunit d, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit e, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit f, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit g, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit j, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit k, mitochondrial
KeywordsATP synthase / FoF1-ATPase / submitochondrial particles / MOTOR PROTEIN
Function / homology
Function and homology information


Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial translation termination / proton channel activity / Mitochondrial protein degradation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis ...Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial translation termination / proton channel activity / Mitochondrial protein degradation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane / lipid binding / mitochondrion
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa ...ATP synthase membrane subunit K / ATP synthase regulation / ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase F(0) complex subunit a / ATP synthase F(0) complex subunit 8 / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase F(0) complex subunit j, mitochondrial / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase F(0) complex subunit e, mitochondrial / ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase F(0) complex subunit g, mitochondrial / ATP synthase F(0) complex subunit k, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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_65579.png

Downloads & links

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Map

FileDownload / File: emd_65579.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 450 pix.
= 654. Å		1.45 Å/pix.
x 450 pix.
= 654. Å		1.45 Å/pix.
x 450 pix.
= 654. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.364651 - 2.489316
Average (Standard dev.)0.00017246268 (±0.03368169)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 654.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65579_msk_1.map
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Half map: #2

Fileemd_65579_half_map_1.map
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Half map: #1

Fileemd_65579_half_map_2.map
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Sample components

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Entire : FoF1-ATPase on the bovine heart submitochondrial particles

EntireName: FoF1-ATPase on the bovine heart submitochondrial particles
Components
  • Complex: FoF1-ATPase on the bovine heart submitochondrial particles
    • Protein or peptide: ATP synthase F(0) complex subunit 8
    • Protein or peptide: ATP synthase F(0) complex subunit C1, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit a
    • Protein or peptide: ATP synthase peripheral stalk subunit b, mitochondrial
    • Protein or peptide: ATP synthase peripheral stalk subunit d, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit e, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit f, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit g, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit j, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit k, mitochondrial

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Supramolecule #1: FoF1-ATPase on the bovine heart submitochondrial particles

SupramoleculeName: FoF1-ATPase on the bovine heart submitochondrial particles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: ATP synthase F(0) complex subunit 8

MacromoleculeName: ATP synthase F(0) complex subunit 8 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 4.901806 KDa
SequenceString:
MPQLDTSTWL TMILSMFLTL FIIFQLKVSK HNFYHNPELT P

UniProtKB: ATP synthase F(0) complex subunit 8

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Macromolecule #2: ATP synthase F(0) complex subunit C1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit C1, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.653034 KDa
SequenceString:
DIDTAAKFIG AGAATVGVAG SGAGIGTVFG SLIIGYARNP SL(M3L)QQLFSYA ILGFALSEAM GLFCLMVAFL ILFAM

UniProtKB: ATP synthase F(0) complex subunit C1, mitochondrial

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Macromolecule #3: ATP synthase F(0) complex subunit a

MacromoleculeName: ATP synthase F(0) complex subunit a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 24.556488 KDa
SequenceString: ENLFTSFITP VILGLPLVTL IVLFPSLLFP TSNRLVSNRF VTLQQWMLQL VSKQMMSIHN SKGQTWTLML MSLILFIGST NLLGLLPHS FTPTTQLSMN LGMAIPLWAG AVITGFRNKT KASLAHFLPQ GTPTPLIPML VIIETISLFI QPMALAVRLT A NITAGHLL ...String:
ENLFTSFITP VILGLPLVTL IVLFPSLLFP TSNRLVSNRF VTLQQWMLQL VSKQMMSIHN SKGQTWTLML MSLILFIGST NLLGLLPHS FTPTTQLSMN LGMAIPLWAG AVITGFRNKT KASLAHFLPQ GTPTPLIPML VIIETISLFI QPMALAVRLT A NITAGHLL IHLIGGATLA LMSISTTTAL ITFTILILLT ILEFAVAMIQ AYVFTLLVSL YLHDNT

UniProtKB: ATP synthase F(0) complex subunit a

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Macromolecule #4: ATP synthase peripheral stalk subunit b, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit b, mitochondrial
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 12.462446 KDa
SequenceString:
PVPPLPEHGG KVRFGLIPEE FFQFLYPKTG VTGPYVLGTG LILYLLSKEI YVITPETFSA ISTIGFLVYI VKKYGASVGE FADKLNEQK IAQLEEVKQA SIKQIQDAID MEK

UniProtKB: ATP synthase peripheral stalk subunit b, mitochondrial

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Macromolecule #5: ATP synthase peripheral stalk subunit d, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit d, mitochondrial
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 6.392311 KDa
SequenceString:
TRIQEYEKEL EKMRNIIPFD QMTIEDLNEV FPETKLDKKK YPYWPHRPIE T

UniProtKB: ATP synthase peripheral stalk subunit d, mitochondrial

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Macromolecule #6: ATP synthase F(0) complex subunit e, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit e, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 8.106361 KDa
SequenceString:
PPVQVSPLIK LGRYSALFLG MAYGAKRYNY LKPRAEEERR LAAEEKKKRD EQKRIERELA EAQEDTILK

UniProtKB: ATP synthase F(0) complex subunit e, mitochondrial

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Macromolecule #7: ATP synthase F(0) complex subunit f, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit f, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 9.827594 KDa
SequenceString:
PLKEKKLLEV KLGELPSWIL MRDFTPSGIA GAFQRGYYRY YNKYVNVKKG SIAGLSMVLA AYVFLNYCRS YKELKHERLR KYH

UniProtKB: ATP synthase F(0) complex subunit f, mitochondrial

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Macromolecule #8: ATP synthase F(0) complex subunit g, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit g, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 8.89648 KDa
SequenceString:
TYSKPRLATF WYYAKVELVP PTPAEIPTAI QSLKKIINSA KTGSFKQLTV KEALLNGLVA TEVWMWFYVG EIIGKRGII

UniProtKB: ATP synthase F(0) complex subunit g, mitochondrial

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Macromolecule #9: ATP synthase F(0) complex subunit j, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit j, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 5.687825 KDa
SequenceString:
LQSLIKKVWI PMKPYYTQAY QEIWVGTGLM AYIVYKIRSA DKRSKALK

UniProtKB: ATP synthase F(0) complex subunit j, mitochondrial

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Macromolecule #10: ATP synthase F(0) complex subunit k, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit k, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 4.124935 KDa
SequenceString:
TGIKKYFNSY TLTGRMNCVL ATYGSIALIV LYFKLR

UniProtKB: ATP synthase F(0) complex subunit k, mitochondrial

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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

Particle selectionNumber selected: 30421492
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 111365
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6zpo


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9w2t:
Cryo-EM structure of Fo domain of FoF1-ATPase monomer state on the bovine heart submitochondrial particles

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