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- PDB-9zfw: Membrane region of Acanthamoeba castellanii mitochondrial ATP syn... -

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Basic information

Entry
Database: PDB / ID: 9zfw
TitleMembrane region of Acanthamoeba castellanii mitochondrial ATP synthase dimer
Components(ATP synthase subunit ...) x 8
KeywordsHYDROLASE / complex V / ATP synthase / OXPHOS complex V
Function / homology
Function and homology information


proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / mitochondrial membrane / mitochondrial inner membrane
Similarity search - Function
ATP synthase YMF19-like, N-terminal / Plant ATP synthase F0 / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / 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.
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / ORFB / ORF25 / ATP synthase subunit a
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsFry, M.Y. / Luce, B.E. / Stefely, J.A. / 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

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit e, mitochondrial
C: ATP synthase subunit g, mitochondrial
E: ATP synthase subunit d, mitochondrial
F: ATP synthase subunit 8, mitochondrial
G: ATP synthase subunit b, mitochondrial
Q: ATP synthase subunit a
X: ATP synthase subunit f, mitochondrial
H: ATP synthase subunit i/j, mitochondrial
B: ATP synthase subunit e, mitochondrial
D: ATP synthase subunit g, mitochondrial
I: ATP synthase subunit d, mitochondrial
J: ATP synthase subunit 8, mitochondrial
K: ATP synthase subunit b, mitochondrial
L: ATP synthase subunit a
M: ATP synthase subunit f, mitochondrial
N: ATP synthase subunit i/j, mitochondrial


Theoretical massNumber of molelcules
Total (without water)322,82716
Polymers322,82716
Non-polymers00
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 ... , 8 types, 16 molecules ABCDEIFJGKQLXMHN

#1: Protein ATP synthase subunit e, mitochondrial


Mass: 11392.696 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACANB06593|subunit e / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: L8GI43
#2: Protein ATP synthase subunit g, mitochondrial


Mass: 12001.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACANB02343 | subunit g / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff
#3: Protein ATP synthase subunit d, mitochondrial


Mass: 56230.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACANB10705|subunit d / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: L8GR48
#4: Protein ATP synthase subunit 8, mitochondrial


Mass: 17424.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACANB15938|subunit 8 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: Q33666
#5: Protein ATP synthase subunit b, mitochondrial


Mass: 14401.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: >ACANB15939|subunit b / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: Q33667
#6: Protein ATP synthase subunit a / F-ATPase protein 6


Mass: 28654.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACANB15943|ATP6 / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: Q37385
#7: Protein ATP synthase subunit f, mitochondrial


Mass: 10670.317 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACANB14194|subunit f / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff / References: UniProt: L8GWE3
#8: Protein ATP synthase subunit i/j, mitochondrial


Mass: 10638.169 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ACANB04724|subunit i/j / Source: (natural) Acanthamoeba castellanii (eukaryote) / Strain: Neff

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Details

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-#5, #7, #6 / 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: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11768 / Symmetry type: POINT
RefinementHighest resolution: 4.23 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310414
ELECTRON MICROSCOPYf_angle_d0.47314128
ELECTRON MICROSCOPYf_dihedral_angle_d4.6971292
ELECTRON MICROSCOPYf_chiral_restr0.0331602
ELECTRON MICROSCOPYf_plane_restr0.0031708

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