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- PDB-9vpd: Cryo-EM structure of the IF1 bound bovine ATP synthase monomer: r... -

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Basic information

Entry
Database: PDB / ID: 9vpd
TitleCryo-EM structure of the IF1 bound bovine ATP synthase monomer: rotary state 1, F1 focused map
Components
  • (ATP synthase F(1) complex subunit ...) x 4
  • (ATP synthase peripheral stalk subunit ...) x 4
  • ATP synthase F(1) complex catalytic subunit beta, mitochondrial
  • ATPase inhibitor, mitochondrial
KeywordsMEMBRANE PROTEIN / ATP synthase/hydrolase / oligomer / membrane bending / mammalian mitochondria / motor protein
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / negative regulation of hydrolase activity / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / heme biosynthetic process / Mitochondrial protein degradation ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / negative regulation of hydrolase activity / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / heme biosynthetic process / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / aerobic respiration / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) ...Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / 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 delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsNakano, A. / Jiko, C. / Yamashita, E. / Yokoyama, K. / Gerle, C.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
CitationJournal: 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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 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
A: ATP synthase F(1) complex subunit alpha, mitochondrial
B: ATP synthase F(1) complex subunit alpha, mitochondrial
C: ATP synthase F(1) complex subunit alpha, mitochondrial
D: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
E: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
F: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
G: ATP synthase F(1) complex subunit gamma, mitochondrial
H: ATP synthase F(1) complex subunit delta, mitochondrial
I: ATP synthase F(1) complex subunit epsilon, mitochondrial
J: ATPase inhibitor, mitochondrial
S: ATP synthase peripheral stalk subunit OSCP, mitochondrial
b: ATP synthase peripheral stalk subunit b, mitochondrial
d: ATP synthase peripheral stalk subunit d, mitochondrial
h: ATP synthase peripheral stalk subunit F6, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)503,67825
Polymers500,75414
Non-polymers2,92511
Water30617
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(1) complex subunit ... , 4 types, 6 molecules ABCGHI

#1: Protein ATP synthase F(1) complex subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 59795.492 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P19483
#3: Protein ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase subunit gamma / ATP synthase F1 subunit gamma / F-ATPase gamma subunit


Mass: 33119.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05631
#4: Protein ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase subunit delta / ATP synthase F1 subunit delta / F-ATPase delta subunit


Mass: 17626.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05630
#5: Protein ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase subunit epsilon / ATPase subunit epsilon / ATP synthase F1 subunit epsilon


Mass: 5793.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05632

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Protein , 2 types, 4 molecules DEFJ

#2: Protein ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase subunit beta / ATP synthase F1 subunit beta


Mass: 56340.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P00829, H+-transporting two-sector ATPase
#6: Protein ATPase inhibitor, mitochondrial / ATPase inhibitory factor 1 (IF1) / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / ...ATPase inhibitory factor 1 (IF1) / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / IF(1) / IF1


Mass: 12326.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P01096

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ATP synthase peripheral stalk subunit ... , 4 types, 4 molecules Sbdh

#7: Protein ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase oligomycin sensitivity conferral protein (OSCP) / ATP synthase subunit O / Oligomycin ...ATP synthase oligomycin sensitivity conferral protein (OSCP) / ATP synthase subunit O / Oligomycin sensitivity conferral protein / OSCP


Mass: 23351.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13621
#8: Protein ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase subunit b / ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase ...ATP synthase subunit b / ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase subunit b / ATPase subunit b


Mass: 28859.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13619
#9: Protein ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase subunit d / ATPase subunit d / ATP synthase peripheral stalk subunit d


Mass: 18719.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13620
#10: Protein ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase subunit F6 / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 12549.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02721

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Non-polymers , 4 types, 28 molecules

#11: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#12: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: IF1 bound bovine ATP synthase monomer isolated from heart muscle tissue mitochondria
Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightValue: 0.6 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.3
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1Topazparticle selection
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 398620 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6YY0

6yy0


Accession code: 6YY0 / Source name: PDB / Type: experimental model

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