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- PDB-9zfu: F1 ATPase from Acanthamoeba castellanii -

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Basic information

Entry
Database: PDB / ID: 9zfu
TitleF1 ATPase from Acanthamoeba castellanii
Components(ATP synthase ...) x 4
KeywordsHYDROLASE / complex V / ATP synthase / OXPHOS complex V
Function / homology
Function and homology information


proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / mitochondrion / ATP binding
Similarity search - Function
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, 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 ...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, 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 subunit beta / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsFry, M.Y. / Luce, B.E. / Stefely, J.A. / Samuelson, J. / Mootha, V.K. / Chao, L.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2026
Title: Acanthamoeba ATP synthase structure reveals the TCA cycle is tethered to OXPHOS.
Authors: Michelle Y Fry / Bridget E Luce / Jonathan A Stefely / Michael Z Chen / Felicia G Deng / Tiana M Issa / / Sarah E Calvo / John Samuelson / Vamsi K Mootha / Luke H Chao /
Abstract: Oxidative phosphorylation (OXPHOS) is a key metabolic process that couples redox energy to ATP production. While some core OXPHOS complex subunits are found across all domains of life, many have ...Oxidative phosphorylation (OXPHOS) is a key metabolic process that couples redox energy to ATP production. While some core OXPHOS complex subunits are found across all domains of life, many have diverged or expanded across evolution-as seen in the protozoan pathogen Acanthamoeba castellanii. By integrating cryo-electron microscopy of unenriched mitochondrial lysate with mass spectrometry proteomics, we resolved the structures of endogenous mitochondrial ATP synthase (complex V), Hsp60, and respiratory complex III from Acanthamoeba. We capture Acanthamoeba ATP synthase in an IF1-inhibited state and reveal how Acanthamoeba-specific subunits and extensions stabilize the molecular machine, which includes a β subunit extension that interfaces with the peripheral stalk. Additionally, we characterize an active malate dehydrogenase (MDH) dimer structurally integrated within the ATP synthase peripheral stalk, thus revealing a direct protein tether between OXPHOS and the tricarboxylic acid cycle. Together, these findings provide structural insight into lineage-specific adaptations in Acanthamoeba that may tune protozoan metabolism.
History
DepositionDec 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / 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 gamma subunit, mitochondrial
R: ATP synthase subunit alpha, mitochondrial
S: ATP synthase subunit alpha, mitochondrial
T: ATP synthase subunit alpha, mitochondrial
U: ATP synthase subunit beta
V: ATP synthase subunit beta
W: ATP synthase subunit beta
B: ATP synthase inhibitory factor 1 (IF1), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,78616
Polymers447,3378
Non-polymers2,4498
Water00
1


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

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Components

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ATP synthase ... , 4 types, 8 molecules ARSTUVWB

#1: Protein ATP synthase gamma subunit, mitochondrial


Mass: 35924.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C
Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
#2: Protein ATP synthase subunit alpha, mitochondrial


Mass: 57668.918 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: ACANB15922 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: Q37380
#3: Protein ATP synthase subunit beta


Mass: 74315.312 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: ACANB02410 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
References: UniProt: L8GXZ0, H+-transporting two-sector ATPase
#4: Protein ATP synthase inhibitory factor 1 (IF1), mitochondrial


Mass: 15459.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB08262 |ATIF1 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff

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Non-polymers , 3 types, 8 molecules

#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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

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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: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 1.3 MDa / Experimental value: NO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Buffer solutionpH: 7.9
Buffer component
IDConc.NameBuffer-ID
150 mMHEPES1
2300 mMsodium chloride1
34 mMmagnesium chloride1
420 uMCalcium Chloride1
51 mMDithiothreitol1
60.5 % (w/v)DDM1
SpecimenConc.: 2.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was not purified. Instead it was solved from imaging mitochondrial lysate.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277.14 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: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 0.99 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCv.4.7.0particle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
5cryoSPARCv.4.7.0CTF correctionPatch CTF estimation
10cryoSPARCinitial Euler assignmentab initio reconstruction
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10863 / Symmetry type: POINT

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