9W2R | pdb_00009w2r

Cryo-EM structure of FoF1-ATPase monomer state 1 on the bovine heart submitochondrial particles (FoF1-1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structures of respiratory supercomplexes and ATP synthase oligomers in mammalian mitochondrial inner membrane.

Nakano, A.Masuya, T.Akisada, S.Ishikawa-Fukuda, M.Mitsuoka, K.Miyoshi, H.Murai, M.Yokoyama, K.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-70578-x
  • Primary Citation Related Structures: 
    9W2R, 9W2S, 9W2T, 9W2U, 9W2V, 9W2X, 9W2Y, 9W2Z

  • PubMed 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 structures of F o F 1 ATP synthase and respiratory supercomplexes (SCs) on sub-mitochondrial particles (SMPs) isolated from bovine heart mitochondria. Most F o F 1 complexes were observed as dimers stabilized by the regulatory factor IF₁, and a tetrameric assembly comprising two F o F 1 -IF₁ dimers arranged linearly was also identified. This finding indicates that the tetrameric units of F o F 1 are present in the mitochondrial inner membrane and contribute to shaping cristae tips in mammalian mitochondria. F o 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 F o F 1 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.


  • Organizational Affiliation
    • Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit 8A [auth 8]66Bos taurusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(1) complex subunit alpha, mitochondrialB [auth A],
C [auth B],
D [auth C]
510Bos taurusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(1) complex catalytic subunit beta, mitochondrialE [auth D],
F [auth E],
G [auth F]
482Bos taurusMutation(s): 0 
EC: 7.1.2.2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(1) complex subunit gamma, mitochondrialH [auth G]273Bos taurusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(1) complex subunit delta, mitochondrialI [auth H]146Bos taurusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(1) complex subunit epsilon, mitochondrialJ [auth I]50Bos taurusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase inhibitor, mitochondrialK [auth J]60Bos taurusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit C1, mitochondrial75Bos taurusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase peripheral stalk subunit OSCP, mitochondrialT [auth S]190Bos taurusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit aU [auth a]226Bos taurusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase peripheral stalk subunit b, mitochondrialV [auth b]214Bos taurusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase peripheral stalk subunit d, mitochondrialW [auth d]160Bos taurusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit e, mitochondrialX [auth e]70Bos taurusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit f, mitochondrialY [auth f]87Bos taurusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit g, mitochondrialZ [auth g]102Bos taurusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase peripheral stalk subunit F6, mitochondrialAA [auth h]76Bos taurusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit j, mitochondrialBA [auth j]60Bos taurusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase F(0) complex subunit k, mitochondrialCA [auth k]57Bos taurusMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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DA [auth A],
FA [auth B],
HA [auth C],
JA [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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LA [auth F]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
EA [auth A],
GA [auth B],
IA [auth C],
KA [auth D],
MA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
L [auth K]
M [auth L]
N [auth M]
O [auth N]
P [auth O]
L [auth K],
M [auth L],
N [auth M],
O [auth N],
P [auth O],
Q [auth P],
R [auth Q],
S [auth R]
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.7

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23H02453
Japan Society for the Promotion of Science (JSPS)Japan25K01958
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-01
    Type: Initial release