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- PDB-9zft: Mitochondrial ATP synthase monomer from Acanthamoeba castellanii -

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Basic information

Entry
Database: PDB / ID: 9zft
TitleMitochondrial ATP synthase monomer from Acanthamoeba castellanii
Components
  • (ATP synthase ...) x 10
  • (unknown protein) x 4
  • ACANB04460
  • ACANB14707
  • ATP synthase, Delta/Epsilon chain, betasandwich domain containing protein
  • F-ATPase gamma subunit,ATP synthase gamma subunit, mitochondrial
  • ORF25
  • ORFB
  • malate dehydrogenase
KeywordsHYDROLASE / complex V / OXPHOS
Function / homology
Function and homology information


(S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / malate metabolic process / 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 / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism ...(S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / malate metabolic process / 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 / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial membrane / mitochondrial inner membrane / mitochondrion / ATP binding
Similarity search - Function
ATP synthase YMF19-like, N-terminal / Plant ATP synthase F0 / Malate dehydrogenase, type 2 / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / ATP synthase, F1 complex, epsilon subunit, mitochondrial ...ATP synthase YMF19-like, N-terminal / Plant ATP synthase F0 / Malate dehydrogenase, type 2 / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, 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, 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 / 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 / NAD(P)-binding domain superfamily / 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 / F-ATPase gamma subunit / ATP synthase subunit epsilon, mitochondrial, putative / Uncharacterized protein / Uncharacterized protein / ATP synthase subunit beta / Uncharacterized protein / ATP synthase, Delta/Epsilon chain, betasandwich domain containing protein / (S)-malate dehydrogenase (NAD(+), oxaloacetate-forming) ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / F-ATPase gamma subunit / ATP synthase subunit epsilon, mitochondrial, putative / Uncharacterized protein / Uncharacterized protein / ATP synthase subunit beta / Uncharacterized protein / ATP synthase, Delta/Epsilon chain, betasandwich domain containing protein / (S)-malate dehydrogenase (NAD(+), oxaloacetate-forming) / ORFB / ORF25 / ATP synthase subunit 9, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit a
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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
6: ATP synthase subunit a
8: ORFB
A: F-ATPase gamma subunit,ATP synthase gamma subunit, mitochondrial
B: ORF25
C: ATP synthase, Delta/Epsilon chain, betasandwich domain containing protein
D: ATP synthase subunit d, mitochondrial
E: ATP synthase inhibitory factor 1 (IF1)
G: ATP synthase OSCP, mitochondrial
H: ATP synthase subunit epsilon, mitochondrial, putative
I: malate dehydrogenase
J: ATP synthase subunit i/j, mitochondrial
K: ATP synthase subunit f, mitochondrial
L: malate dehydrogenase
M: ACANB14707
P: ATP synthase subunit 9, mitochondrial
Q: ATP synthase subunit 9, mitochondrial
R: ATP synthase subunit 9, mitochondrial
S: ATP synthase subunit 9, mitochondrial
T: ATP synthase subunit 9, mitochondrial
U: ATP synthase subunit 9, mitochondrial
V: ATP synthase subunit 9, mitochondrial
W: ATP synthase subunit 9, mitochondrial
X: ATP synthase subunit 9, mitochondrial
Z: ACANB04460
a: ATP synthase subunit alpha, mitochondrial
b: ATP synthase subunit alpha, mitochondrial
c: ATP synthase subunit alpha, mitochondrial
d: ATP synthase subunit beta
e: ATP synthase subunit beta
f: ATP synthase subunit beta
1: unknown protein
2: unknown protein
3: unknown protein
5: unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)875,50642
Polymers873,05734
Non-polymers2,4498
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 10 types, 22 molecules 6DEGHJKPQRSTUVWXabcdef

#1: Protein ATP synthase subunit a / F-ATPase protein 6


Mass: 24183.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB15943 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: Q37385
#6: Protein ATP synthase subunit d, mitochondrial


Mass: 56230.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB10705 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: L8GR48
#7: Protein ATP synthase inhibitory factor 1 (IF1)


Mass: 15459.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB08262 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
#8: Protein ATP synthase OSCP, mitochondrial


Mass: 48823.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB01783 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
#9: Protein/peptide ATP synthase subunit epsilon, mitochondrial, putative


Mass: 4988.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB12077 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: L8GI75
#11: Protein ATP synthase subunit i/j, mitochondrial


Mass: 10638.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB04724 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
#12: Protein ATP synthase subunit f, mitochondrial


Mass: 10670.317 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB14194 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: L8GWE3
#14: Protein
ATP synthase subunit 9, mitochondrial / Lipid-binding protein


Mass: 8249.944 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Details: ACANB15917 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: Q37377
#16: 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
#17: 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

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Protein , 9 types, 10 molecules 8ABCILMZ12

#2: Protein ORFB


Mass: 17424.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB15938 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: Q33666
#3: Protein F-ATPase gamma subunit,ATP synthase gamma subunit, mitochondrial


Mass: 35924.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB07530,ACANB07530 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: L8GG83
#4: Protein ORF25


Mass: 14401.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB15939 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: Q33667
#5: Protein ATP synthase, Delta/Epsilon chain, betasandwich domain containing protein


Mass: 20395.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB02409 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: L8H026
#10: Protein malate dehydrogenase


Mass: 49101.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACANB11954 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
References: UniProt: L8HFT9, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
#13: Protein ACANB14707


Mass: 10217.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB14707 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
#15: Protein ACANB04460


Mass: 15561.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACANB04460 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: L8GY60
#18: Protein unknown protein


Mass: 6060.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
#19: Protein unknown protein


Mass: 11251.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff

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Protein/peptide , 2 types, 2 molecules 35

#20: Protein/peptide unknown protein


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
#21: Protein/peptide unknown protein


Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff

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Non-polymers , 3 types, 8 molecules

#22: 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
#23: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#24: 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-#21 / 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 mMCalcium 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: BRIGHT 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)
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCv.4.7.0CTF correctionPatch CTF estimation
9cryoSPARCinitial Euler assignmentab initio reconstruction
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10863 / Symmetry type: POINT

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