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- PDB-9bym: Cryo-EM structure of ATP synthase non-stator state -

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Basic information

Entry
Database: PDB / ID: 9bym
TitleCryo-EM structure of ATP synthase non-stator state
Components
  • (ATP synthase F1 subunit ...) x 2
  • (ATP synthase subunit ...) x 3
  • ATP synthase lipid-binding protein
  • ATPase inhibitor, mitochondrial
KeywordsMEMBRANE PROTEIN / heart / ATP synthase
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex binding / regulation of protein targeting to mitochondrion / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / mitochondrial depolarization / ATPase inhibitor activity / positive regulation of type 2 mitophagy / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...mitochondrial proton-transporting ATP synthase complex binding / regulation of protein targeting to mitochondrion / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / mitochondrial depolarization / ATPase inhibitor activity / positive regulation of type 2 mitophagy / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / heme biosynthetic process / proton-transporting two-sector ATPase complex, proton-transporting domain / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / reactive oxygen species metabolic process / erythrocyte differentiation / ATPase binding / calmodulin binding / mitochondrial inner membrane / intracellular membrane-bounded organelle / lipid binding / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal ...Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / 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, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain 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 subunit delta, mitochondrial / ATP synthase subunit gamma / ATP synthase subunit beta / ATP synthase F1 subunit epsilon / ATP synthase lipid-binding protein / ATP synthase subunit alpha / ATPase inhibitor, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsZhang, Z. / Maharjan, R. / Tringides, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of ATP synthase non-stator state
Authors: Zhang, Z. / Maharjan, R. / Tringides, M.
History
DepositionMay 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
J: ATPase inhibitor, mitochondrial
G: ATP synthase subunit gamma
H: ATP synthase F1 subunit delta
I: ATP synthase F1 subunit epsilon
K: ATP synthase lipid-binding protein
L: ATP synthase lipid-binding protein
N: ATP synthase lipid-binding protein
O: ATP synthase lipid-binding protein
P: ATP synthase lipid-binding protein
Q: ATP synthase lipid-binding protein
R: ATP synthase lipid-binding protein
M: ATP synthase lipid-binding protein
B: ATP synthase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)555,16327
Polymers552,69018
Non-polymers2,4739
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 subunit ... , 3 types, 7 molecules ACBDEFG

#1: Protein ATP synthase subunit alpha


Mass: 59502.258 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1XYK3
#2: Protein ATP synthase subunit beta


Mass: 60893.625 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A8D1JU29, H+-transporting two-sector ATPase
#4: Protein ATP synthase subunit gamma


Mass: 30252.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0YCC0

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Protein , 2 types, 9 molecules JKLNOPQRM

#3: Protein ATPase inhibitor, mitochondrial / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / IF(1) / IF1


Mass: 12209.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q29307
#7: Protein
ATP synthase lipid-binding protein / ATPase protein 9 / ATPase subunit c


Mass: 14596.909 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1WGE8

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ATP synthase F1 subunit ... , 2 types, 2 molecules HI

#5: Protein ATP synthase F1 subunit delta


Mass: 17489.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VPE5
#6: Protein ATP synthase F1 subunit epsilon


Mass: 14774.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1L782

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Non-polymers , 3 types, 9 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN
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: Cryo-EM structure of ATP synthase non-stator state / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19085 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00330324
ELECTRON MICROSCOPYf_angle_d0.50441015
ELECTRON MICROSCOPYf_dihedral_angle_d12.86911132
ELECTRON MICROSCOPYf_chiral_restr0.044786
ELECTRON MICROSCOPYf_plane_restr0.0045279

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