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- EMDB-74154: F1 ATPase from Acanthamoeba castellanii -

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Basic information

Entry
Database: EMDB / ID: EMD-74154
TitleF1 ATPase from Acanthamoeba castellanii
Map data
Sample
  • Complex: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
    • Protein or peptide: ATP synthase gamma subunit, mitochondrial
    • Protein or peptide: ATP synthase subunit alpha, mitochondrial
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase inhibitory factor 1 (IF1), mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordscomplex V / ATP synthase / OXPHOS complex V / HYDROLASE
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
ATP synthase subunit beta / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsFry MY / Luce BE / Stefely JA / Samuelson J / 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_74154.png

Downloads & links

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Map

FileDownload / File: emd_74154.map.gz / Format: CCP4 / Size: 325 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 440 pix.
= 361.68 Å		0.82 Å/pix.
x 440 pix.
= 361.68 Å		0.82 Å/pix.
x 440 pix.
= 361.68 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: 0.135
Minimum - Maximum-0.29582518 - 0.5534082
Average (Standard dev.)0.0018663503 (±0.024034508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 361.68002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_74154_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74154_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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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 gamma subunit, mitochondrial
    • Protein or peptide: ATP synthase subunit alpha, mitochondrial
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase inhibitory factor 1 (IF1), mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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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-#4
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 1.3 MDa

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Macromolecule #1: ATP synthase gamma subunit, mitochondrial

MacromoleculeName: ATP synthase gamma subunit, mitochondrial / type: protein_or_peptide / ID: 1
Details: ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C,ACANB07530 | ATP5F1C
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 35.924637 KDa
SequenceString: MRRVSSVGLR TSAFELRTSA VQTARTFERN ELGPVGVRHY PGNLKELRLR LVAIKNIKKI TSTMKMIAAA KLNKAQAVLF KTRPYSESS QRFIQEFFPS PQEGEPNPAE EASAGKHLIV AVTSDRGLCG GVNSSIIKAS AAVLRNHPEN TQLFLVGEKS K AALQREYA ...String:
MRRVSSVGLR TSAFELRTSA VQTARTFERN ELGPVGVRHY PGNLKELRLR LVAIKNIKKI TSTMKMIAAA KLNKAQAVLF KTRPYSESS QRFIQEFFPS PQEGEPNPAE EASAGKHLIV AVTSDRGLCG GVNSSIIKAS AAVLRNHPEN TQLFLVGEKS K AALQREYA NAIVYAVSEV GANKKTSFTE VAQVAELIAR QPADNVTLLY NHFNSVLSFT TTRKVFPSPK TFVEAERKFS AY EFEGSHE EILADYWQFS VASQLYSAIT ESQTAEVATR MTSMDNATKN ASEVLNKLTI KYNRTRQAAI TTELTEIVSG AAA IEEASS

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Macromolecule #2: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 2 / Details: ACANB15922 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 57.668918 KDa
SequenceString: MKKYQFLKSN LLQNQNINEL FLQYLKNDSN IGVIKSIVDG VVIIEGLSNV KAGEMLQFSN DIQGMALNLN SETVSAVLFG DETKIKPGE YVEGTGNIIS VPVGMSLLGR VVNALGQPID NKGDFPGSEL KQVEVKAPGI ITRQSVNEPM ITGVKAIDCL V PVGRGQRE ...String:
MKKYQFLKSN LLQNQNINEL FLQYLKNDSN IGVIKSIVDG VVIIEGLSNV KAGEMLQFSN DIQGMALNLN SETVSAVLFG DETKIKPGE YVEGTGNIIS VPVGMSLLGR VVNALGQPID NKGDFPGSEL KQVEVKAPGI ITRQSVNEPM ITGVKAIDCL V PVGRGQRE LVIGDRQTGK TSICLDAVLN QKYENSKNKK NALYCIYTAI GQKRSSISKL VTLLEKTNSL EYSIIVAATA SE AAPLQYL APYTGCVIGE YFRDNGKHAL IIYDDLSKQA VAYRQMSLLL RRPPGREAYP GDIFYLHSRL LERAAKLNKN FGG GSLTAL PVVETQAGDV SAYIPTNVIS ITDGQIFLET NLFYNGIRPA VNVGLSVSRV GSAAQILAIK KLAGSLKLEL AQYR EALSF AQFGSDLDET TKNLLSRGNM LTELLNQNRF TPIPIENQFV LMYSGIKGFL TNVNNKVIRS YENELFNRIS NYSVF NTNV ILLSNNEYYK KKNNNNVVAF FISYFKFITT NIFGFSAK

UniProtKB: ATP synthase subunit alpha, mitochondrial

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Macromolecule #3: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 3 / Details: ACANB02410 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 74.315312 KDa
SequenceString: MLRNFSKRAL PRTALSRGLA TRTAAGLRQG ANTTLATSSA PSKYAMWGSR TLATQPEPKT ASKAEAESQA VDTDGKIVQI IGAVVDVKF PEDALPPILS ALEIQDHNIK LILEVAQHLG RGVCRTIAMD ATEGLQRGQR VKDLKGPITV PVGAATLGRI I NVIGDPID ...String:
MLRNFSKRAL PRTALSRGLA TRTAAGLRQG ANTTLATSSA PSKYAMWGSR TLATQPEPKT ASKAEAESQA VDTDGKIVQI IGAVVDVKF PEDALPPILS ALEIQDHNIK LILEVAQHLG RGVCRTIAMD ATEGLQRGQR VKDLKGPITV PVGAATLGRI I NVIGDPID EKGPIYSNKR NPIHAAPPTL TEQGASDQIL VTGIKVVDLL APYAKGGKIG LFGGAGVGKT VLIMELINNI AK AHGGFSV FAGVGERTRE GNDLYHEMIT SEVIKLKDPK TLKEGDHIGE GSKAALVYGQ MNEPPGARAR VALTGLAVAE YFR DEEGQD VLLFIDNIFR FTQAGSEVSA LLGRIPSAVG YQPTLATDMG QLQERITTTM KGSITSVQAI YVPADDLTDP APAT TFAHL DATTVLSRQI AELGIYPAVD PLDSTSRMMD AEIVGKEHYD VARAVQKTLQ DYKSLQDIIA ILGMDELSEE DKATV YRAR KIQKFLSQPF QVAQVFTGFE GKFVSLKDTI SGFKSILEGK YDHLPEPAFY MVGDIEEVVQ KAQKLAADLG GGSAAK KDG KDASGAKVSG KRELTLDAFN DPSYPELKEG DFELNEKSFR VFAEYTKNVA IPYARDHELK EFPEDAAKIK AKYDNIL SK IDGETDELVK ELHDASQKHD AERKRKEQEA ALKAQKAAAP QAAAH

UniProtKB: ATP synthase subunit beta

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Macromolecule #4: ATP synthase inhibitory factor 1 (IF1), mitochondrial

MacromoleculeName: ATP synthase inhibitory factor 1 (IF1), mitochondrial / type: protein_or_peptide / ID: 4 / Details: ACANB08262 |ATIF1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 15.459335 KDa
SequenceString:
MMRRAATRSA LCRPSFAPTA ARGYSSVLEA GGRLGEREKA VEDRAIRGHD LELLKKLRDT LGIQENQPIP ETVVSQVSSS SSSLNPFAQ RAQSQQPSSS SHNDEPLTRG EFLEFRREIV QRLRNLEDDI MDLQTRRK

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10863
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC / Software - details: ab initio reconstruction
Final angle assignmentType: PROJECTION MATCHING

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