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- EMDB-74156: Membrane region of Acanthamoeba castellanii mitochondrial ATP syn... -

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Basic information

Entry
Database: EMDB / ID: EMD-74156
TitleMembrane region of Acanthamoeba castellanii mitochondrial ATP synthase dimer
Map data
Sample
  • Complex: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
    • Protein or peptide: ATP synthase subunit e, mitochondrial
    • Protein or peptide: ATP synthase subunit g, mitochondrial
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit 8, mitochondrial
    • Protein or peptide: ATP synthase subunit b, mitochondrial
    • Protein or peptide: ATP synthase subunit f, mitochondrial
    • Protein or peptide: ATP synthase subunit a
  • Protein or peptide: ATP synthase subunit i/j, mitochondrial
Keywordscomplex V / ATP synthase / OXPHOS complex V / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsFry MY / Luce BE / Stefely JA / Mootha VK / Chao LH
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74156.png

Downloads & links

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Map

FileDownload / File: emd_74156.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å		0.82 Å/pix.
x 400 pix.
= 328.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.077
Minimum - Maximum-0.10954116 - 0.26010373
Average (Standard dev.)0.0019701403 (±0.012531517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_74156_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74156_half_map_2.map
Projections & Slices
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Sample components

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Entire : Acanthamoeba castellanii OXPHOS complex III intermediate assembly...

EntireName: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
Components
  • Complex: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
    • Protein or peptide: ATP synthase subunit e, mitochondrial
    • Protein or peptide: ATP synthase subunit g, mitochondrial
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase subunit 8, mitochondrial
    • Protein or peptide: ATP synthase subunit b, mitochondrial
    • Protein or peptide: ATP synthase subunit f, mitochondrial
    • Protein or peptide: ATP synthase subunit a
  • Protein or peptide: ATP synthase subunit i/j, mitochondrial

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Supramolecule #1: Acanthamoeba castellanii OXPHOS complex III intermediate assembly...

SupramoleculeName: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5, #7, #6
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 1.3 MDa

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Macromolecule #1: ATP synthase subunit e, mitochondrial

MacromoleculeName: ATP synthase subunit e, mitochondrial / type: protein_or_peptide / ID: 1 / Details: ACANB06593|subunit e / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 11.392696 KDa
SequenceString:
MATPLQVPCG CRNSLQSFGA AAAFTVAFVW TSQSVQVKRN AYFSNLKSEI DTLKKKNHDL EHEVELLKNP PEPKEAHTDF AADFESGNI DFEKILEQVA SDH

UniProtKB: Uncharacterized protein

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Macromolecule #2: ATP synthase subunit g, mitochondrial

MacromoleculeName: ATP synthase subunit g, mitochondrial / type: protein_or_peptide / ID: 2 / Details: ACANB02343 | subunit g / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 12.001693 KDa
SequenceString:
MNRLCGSLAK GAQKFQALEQ STTSCACNKQ LYGYLGTQFG CWSNRWQAFP ADAKALWRRV ITGQITVGEV GRGVRASTPI LLAALAGNF LGRGEFLYSP IVGASYTYPE Y

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Macromolecule #3: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 3 / Details: ACANB10705|subunit d / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 56.230902 KDa
SequenceString: MRRISRVVAS SARGTALNKS SRTAAVFSRG YAAPETPQTD FKVTDAGIRV YAHGVVHDMN FLGDLPADAQ EVLSGKEWVP QSVSDFTAR WEKDAPELAN QARQLESLIT KFEKDPVQFG KSEAYLRDIA IHTTLERAAA RDVSPVEIAL THFWTAYSEV P SGGKLRES ...String:
MRRISRVVAS SARGTALNKS SRTAAVFSRG YAAPETPQTD FKVTDAGIRV YAHGVVHDMN FLGDLPADAQ EVLSGKEWVP QSVSDFTAR WEKDAPELAN QARQLESLIT KFEKDPVQFG KSEAYLRDIA IHTTLERAAA RDVSPVEIAL THFWTAYSEV P SGGKLRES APTQLERVKA FLQSKKDPEL SAQNSRARKT AAIVKFVQAS SAEDKAAAAA LLLGSEKGQA LKAALKGVND AA KKEQIVK QHLQWDEATQ AAAELTQRHP EFTELKEVLA HFPPLVHHIG EPSAVQYRFK HATDKAYKKW QQNYSLTSSD EVT EKDPLL KNLRELLYSG KPANTVADAK KAQALQRSFP GLLFSRDVES FSNFVRKDEE VKSQLSTIYE DSLKEYPNDP ALAV PKDLD QRVKLWSKHT QELADVQQQW LDAKIAFIDA KIQEGMVQMD KFVNGTVDDI LADHPEWEKE IEDDIANHRW DPEME KKEY DNALHHYYEH HTVHA

UniProtKB: Uncharacterized protein

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Macromolecule #4: ATP synthase subunit 8, mitochondrial

MacromoleculeName: ATP synthase subunit 8, mitochondrial / type: protein_or_peptide / ID: 4 / Details: ACANB15938|subunit 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 17.42434 KDa
SequenceString:
MPQLDKLSFA TQYFWLTLFF FGLYFLSVNF FVILVFKNLK LRNIIYKIWY FFLYRFDYVD YNNKHKSLVN TSFSFIYYTL YINFFILTK INFIFEKTKS IINKTQTLNQ SQRLLMISLL NNFLNSNSVD FVKKFQELNI DEI

UniProtKB: ORFB

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Macromolecule #5: ATP synthase subunit b, mitochondrial

MacromoleculeName: ATP synthase subunit b, mitochondrial / type: protein_or_peptide / ID: 5 / Details: >ACANB15939|subunit b / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 14.401209 KDa
SequenceString:
MKYSILLFFT LFAINNLLHY ISEKVIIVIF IVFLFFLMGF LSNIINSEFK SKIDYILNDI NAYVNVVFNF LYINKLFYLN LKSLKTGFL SLNSILGKKI DSLKFYTTLS NKLNAISSTT VLLLK

UniProtKB: ORF25

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Macromolecule #6: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 6 / Details: ACANB15943|ATP6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 28.654133 KDa
SequenceString: MIFNPLEQFR ISVLQKLFFG NIDISITNNT IILFVILIGF TFLFYVNYST NTYIPSKWQY AVENIYLFVL QLFKQQINNI VALKYFPLV LFVFSFILFA NLIGLLPYGF TITGHIIFTF QIAFSLFFGI TLINFFNNKT EFFNLFVPSG VPKPLIPFLV V IEVVSYLI ...String:
MIFNPLEQFR ISVLQKLFFG NIDISITNNT IILFVILIGF TFLFYVNYST NTYIPSKWQY AVENIYLFVL QLFKQQINNI VALKYFPLV LFVFSFILFA NLIGLLPYGF TITGHIIFTF QIAFSLFFGI TLINFFNNKT EFFNLFVPSG VPKPLIPFLV V IEVVSYLI RPFSLSVRLF ANMLAGHTLL NILSAFIFNV FKKYALISFL PLLFIVFIIV LEFCIAIVQA YIFSILTCIY LN DIYNTSH

UniProtKB: ATP synthase subunit a

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Macromolecule #7: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 7 / Details: ACANB14194|subunit f / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 10.670317 KDa
SequenceString:
MSRSLITRSL PLRSSSHGAL GGARPVFSEV PLKEVPSYVR LHVLGNTRRL TKEFVQWYWR TYFHAGKADP IIHGILLVSG VGYLLHNHW HGSHP

UniProtKB: Uncharacterized protein

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Macromolecule #8: ATP synthase subunit i/j, mitochondrial

MacromoleculeName: ATP synthase subunit i/j, mitochondrial / type: protein_or_peptide / ID: 8 / Details: ACANB04724|subunit i/j / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 10.638169 KDa
SequenceString:
MSARNFGLTE GEIQELKKRP YPRFAPAPMQ RLISQAKVIW PFAVGWAVTL FLYSRIPISD DDRAKSHYQY QLDVLDGKIK PEDHPIHGH HGH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.25 mg/mL
BufferpH: 7.9
Component:
ConcentrationName
50.0 mMHEPES
300.0 mMsodium chloride
4.0 mMmagnesium chloride
20.0 uMCalcium Chloride
1.0 mMDithiothreitol
0.5 % (w/v)DDM
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.14 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was not purified. Instead it was solved from imaging mitochondrial lysate.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 0.99 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v.4.7.0) / Software - details: Patch CTF estimation / Type: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 11768
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC / Software - details: ab initio reconstruction
Final angle assignmentType: PROJECTION MATCHING

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