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- PDB-9w2t: Cryo-EM structure of Fo domain of FoF1-ATPase monomer state on th... -

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Basic information

Entry
Database: PDB / ID: 9w2t
TitleCryo-EM structure of Fo domain of FoF1-ATPase monomer state on the bovine heart submitochondrial particles
Components
  • (ATP synthase F(0) complex subunit ...) x 8
  • (ATP synthase peripheral stalk subunit ...) x 2
KeywordsMOTOR PROTEIN / ATP synthase / FoF1-ATPase / submitochondrial particles
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)
MethodELECTRON MICROSCOPY / single 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, 3items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
8: ATP synthase F(0) complex subunit 8
K: ATP synthase F(0) complex subunit C1, mitochondrial
L: ATP synthase F(0) complex subunit C1, mitochondrial
M: ATP synthase F(0) complex subunit C1, mitochondrial
N: ATP synthase F(0) complex subunit C1, mitochondrial
O: ATP synthase F(0) complex subunit C1, mitochondrial
P: ATP synthase F(0) complex subunit C1, mitochondrial
Q: ATP synthase F(0) complex subunit C1, mitochondrial
R: ATP synthase F(0) complex subunit C1, mitochondrial
a: ATP synthase F(0) complex subunit a
b: ATP synthase peripheral stalk subunit b, mitochondrial
d: ATP synthase peripheral stalk subunit d, mitochondrial
e: ATP synthase F(0) complex subunit e, mitochondrial
f: ATP synthase F(0) complex subunit f, mitochondrial
g: ATP synthase F(0) complex subunit g, mitochondrial
j: ATP synthase F(0) complex subunit j, mitochondrial
k: ATP synthase F(0) complex subunit k, mitochondrial


Theoretical massNumber of molelcules
Total (without water)146,18117
Polymers146,18117
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase F(0) complex subunit ... , 8 types, 15 molecules 8KLMNOPQRaefgjk

#1: Protein/peptide ATP synthase F(0) complex subunit 8 / A6L / F-ATPase subunit 8


Mass: 4901.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P03929
#2: Protein
ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase ...ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase proteolipid P1 / ATPase protein 9 / ATPase subunit c / Proton-conducting channel / ATP synthase F(0) complex subunit c


Mass: 7653.034 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P32876
#3: Protein ATP synthase F(0) complex subunit a / F-ATPase protein 6 / Proton-conducting channel / ATP synthase F(0) complex subunit a


Mass: 24556.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00847
#6: Protein ATP synthase F(0) complex subunit e, mitochondrial / ATPase subunit e / ATP synthase membrane subunit e


Mass: 8106.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q00361
#7: Protein ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase membrane subunit f


Mass: 9827.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q28851
#8: Protein ATP synthase F(0) complex subunit g, mitochondrial / ATPase subunit g / ATP synthase membrane subunit g


Mass: 8896.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q28852
#9: Protein/peptide ATP synthase F(0) complex subunit j, mitochondrial / 6.8 kDa mitochondrial proteolipid / 6.8 kDa mitochondrial proteolipid protein / MLQ


Mass: 5687.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P14790
#10: Protein/peptide ATP synthase F(0) complex subunit k, mitochondrial / ATP synthase membrane subunit DAPIT / mitochondrial / Diabetes-associated protein in insulin- ...ATP synthase membrane subunit DAPIT / mitochondrial / Diabetes-associated protein in insulin-sensitive tissues / Up-regulated during skeletal muscle growth protein 5


Mass: 4124.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3ZBI7

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ATP synthase peripheral stalk subunit ... , 2 types, 2 molecules bd

#4: Protein ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase peripheral stalk-membrane ...ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase subunit b / ATPase subunit b


Mass: 12462.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13619
#5: Protein ATP synthase peripheral stalk subunit d, mitochondrial / ATPase subunit d / ATP synthase peripheral stalk subunit d


Mass: 6392.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13620

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FoF1-ATPase on the bovine heart submitochondrial particles
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.60 MDa / Experimental value: YES
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
7Coot0.9.8.95model fitting
8ISOLDE1.9model fitting
10PHENIX1.21.2_5419model refinement
14cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 30421492
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111365 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6ZPO

6zpo


Accession code: 6ZPO / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410238
ELECTRON MICROSCOPYf_angle_d0.71913862
ELECTRON MICROSCOPYf_dihedral_angle_d5.7241430
ELECTRON MICROSCOPYf_chiral_restr0.0421622
ELECTRON MICROSCOPYf_plane_restr0.0041694

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