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- EMDB-74153: Mitochondrial ATP synthase monomer from Acanthamoeba castellanii -

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Basic information

Entry
Database: EMDB / ID: EMD-74153
TitleMitochondrial ATP synthase monomer from Acanthamoeba castellanii
Map data
Sample
  • Complex: Acanthamoeba castellanii OXPHOS complex III intermediate assembly state missing the Rieske subunit
    • Protein or peptide: x 21 types
  • Ligand: x 3 types
Keywordscomplex V / OXPHOS / HYDROLASE
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
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 ...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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 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_74153.png

Downloads & links

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Map

FileDownload / File: emd_74153.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.17493598 - 0.40732962
Average (Standard dev.)0.0018700152 (±0.018599784)
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: #1

Fileemd_74153_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_74153_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 a
    • Protein or peptide: ORFB
    • Protein or peptide: F-ATPase gamma subunit,ATP synthase gamma subunit, mitochondrial
    • Protein or peptide: ORF25
    • Protein or peptide: ATP synthase, Delta/Epsilon chain, betasandwich domain containing protein
    • Protein or peptide: ATP synthase subunit d, mitochondrial
    • Protein or peptide: ATP synthase inhibitory factor 1 (IF1)
    • Protein or peptide: ATP synthase OSCP, mitochondrial
    • Protein or peptide: ATP synthase subunit epsilon, mitochondrial, putative
    • Protein or peptide: malate dehydrogenase
    • Protein or peptide: ATP synthase subunit i/j, mitochondrial
    • Protein or peptide: ATP synthase subunit f, mitochondrial
    • Protein or peptide: ACANB14707
    • Protein or peptide: ATP synthase subunit 9, mitochondrial
    • Protein or peptide: ACANB04460
    • Protein or peptide: ATP synthase subunit alpha, mitochondrial
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: unknown protein
    • Protein or peptide: unknown protein
    • Protein or peptide: unknown protein
    • Protein or peptide: unknown protein
  • 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-#21
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 1.3 MDa

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Macromolecule #1: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 1 / Details: ACANB15943 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 24.183861 KDa
SequenceString: NTIILFVILI GFTFLFYVNY STNTYIPSKW QYAVENIYLF VLQLFKQQIN NIVALKYFPL VLFVFSFILF ANLIGLLPYG FTITGHIIF TFQIAFSLFF GITLINFFNN KTEFPLIPFL VVIEVVSYLI RPFSLSVRLF ANMLAGHTLL NILSAFIFNV F KKYALISF ...String:
NTIILFVILI GFTFLFYVNY STNTYIPSKW QYAVENIYLF VLQLFKQQIN NIVALKYFPL VLFVFSFILF ANLIGLLPYG FTITGHIIF TFQIAFSLFF GITLINFFNN KTEFPLIPFL VVIEVVSYLI RPFSLSVRLF ANMLAGHTLL NILSAFIFNV F KKYALISF LPLLFIVFII VLEFCIAIVQ AYIFSILTCI YLNDIYNTSH

UniProtKB: ATP synthase subunit a

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Macromolecule #2: ORFB

MacromoleculeName: ORFB / type: protein_or_peptide / ID: 2 / Details: ACANB15938 / Number of copies: 1 / 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 #3: F-ATPase gamma subunit,ATP synthase gamma subunit, mitochondrial

MacromoleculeName: F-ATPase gamma subunit,ATP synthase gamma subunit, mitochondrial
type: protein_or_peptide / ID: 3 / Details: ACANB07530,ACANB07530 / 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

UniProtKB: F-ATPase gamma subunit

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Macromolecule #4: ORF25

MacromoleculeName: ORF25 / type: protein_or_peptide / ID: 4 / Details: ACANB15939 / Number of copies: 1 / 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 #5: ATP synthase, Delta/Epsilon chain, betasandwich domain containing...

MacromoleculeName: ATP synthase, Delta/Epsilon chain, betasandwich domain containing protein
type: protein_or_peptide / ID: 5 / Details: ACANB02409 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 20.39524 KDa
SequenceString:
MRRISASSRV LGMSAAAGGR FAPRTASVLT TTTRRSYATD DAQREAHEKA VKEGKLIFTL ACPHETLINA EPVRIATVPS ATGDMGILA HHVPTIAQLK PGVVKVTKFD ESGATRDADY FISGGFVTVY PDSHCNVNVV EAFPLDQLDP EKAKKGLEDF T KELASASD AEAKTVATIG VEVYKAMCSA LKV

UniProtKB: ATP synthase, Delta/Epsilon chain, betasandwich domain containing protein

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Macromolecule #6: ATP synthase subunit d, mitochondrial

MacromoleculeName: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 6 / Details: ACANB10705 / Number of copies: 1 / 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 #7: ATP synthase inhibitory factor 1 (IF1)

MacromoleculeName: ATP synthase inhibitory factor 1 (IF1) / type: protein_or_peptide / ID: 7 / Details: ACANB08262 / 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 #8: ATP synthase OSCP, mitochondrial

MacromoleculeName: ATP synthase OSCP, mitochondrial / type: protein_or_peptide / ID: 8 / Details: ACANB01783 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 48.823629 KDa
SequenceString: MYASRSSGMA CRSRLASRVA PRMGNAARLV SARGFSQTLV TQQKKGEATT AAPVFKIDEE FDDYKDVTAS NEQVEKNYRE PPVQVTSGK HGEFASTLYA TASVLNAVED VERDLKWLVD ASQTIPMFQQ FLSSGLPDKK VMRKLLQGVL KGADFHRLTQ K FLVTELLE ...String:
MYASRSSGMA CRSRLASRVA PRMGNAARLV SARGFSQTLV TQQKKGEATT AAPVFKIDEE FDDYKDVTAS NEQVEKNYRE PPVQVTSGK HGEFASTLYA TASVLNAVED VERDLKWLVD ASQTIPMFQQ FLSSGLPDKK VMRKLLQGVL KGADFHRLTQ K FLVTELLE AGELKLVPDI AAVYAQIMKA HRKEVPVVFT FASLPDKDFL TRQIERVKKY RLEADATPMW EFKINPALIG GF TVEVGSN YKGNFALSSQ FDLMRQQLKQ AEDKWERVRP KELHINSFDT SSLFAPLSGV KITAADLDKT LADVLGSKKE AFQ AADLDR TLKQALEDAQ RDAGFSGDYE KNVLEQTRNL DFEKLKTVKQ LDLAQHEKHL MQKHNIADND AEGKRKVKAK IEEL KRFKE LDTSFIGEVL KKHQPETYKK YQSVFQ

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Macromolecule #9: ATP synthase subunit epsilon, mitochondrial, putative

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial, putative / type: protein_or_peptide / ID: 9 / Details: ACANB12077 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 4.988681 KDa
SequenceString:
LKEPFRAKAA ERDSVNMKVE QWILGKGQDK VDVKRANEIA GSAGH

UniProtKB: ATP synthase subunit epsilon, mitochondrial, putative

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Macromolecule #10: malate dehydrogenase

MacromoleculeName: malate dehydrogenase / type: protein_or_peptide / ID: 10 / Details: ACANB11954 / Number of copies: 2 / Enantiomer: LEVO
EC number: (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 49.101977 KDa
SequenceString: MRRGLSTVSR SATVFGKQAC LASSTLRVDR RAYATSPEDA ALEAQIEKVL DLVKKQGNLG SEKLTVRKLT ELRQTVPEID RALSSVGDS AVKYMAELEK PGAGPLSAVP PVRVTVTGAA GAIGYAMLFR IASGEMLGKH QPVILQLLEL EPAMKALEGV I MELKDCAF ...String:
MRRGLSTVSR SATVFGKQAC LASSTLRVDR RAYATSPEDA ALEAQIEKVL DLVKKQGNLG SEKLTVRKLT ELRQTVPEID RALSSVGDS AVKYMAELEK PGAGPLSAVP PVRVTVTGAA GAIGYAMLFR IASGEMLGKH QPVILQLLEL EPAMKALEGV I MELKDCAF PLLHGVTASS DVNKAFEGAD FAMLVGAKPR TKGMERGDLL KENANIFSVQ GKALNKVANR DTLRVCVVGN PA NTNALIA SANAPNIHPR RFTAMTRLDH NRGIAQLADK LKCKVTDIER FAIWGNHSAT QYPDISHTQI NGKWAKDLVD EKW VKDTFI PDVQQRGAAI IAARGSSSAA SAANAAIEHM RDWVKGTNGQ WTSMGVWTGN GKVGDYGTSP DIYYSFPVVC ADGE YTIVQ NVPVDKFSAE RMQKTNDELV SEKNGVGELA KRTTDPAALL KEQYKGGKQ

UniProtKB: (S)-malate dehydrogenase (NAD(+), oxaloacetate-forming)

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Macromolecule #11: ATP synthase subunit i/j, mitochondrial

MacromoleculeName: ATP synthase subunit i/j, mitochondrial / type: protein_or_peptide / ID: 11 / Details: ACANB04724 / Number of copies: 1 / 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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Macromolecule #12: ATP synthase subunit f, mitochondrial

MacromoleculeName: ATP synthase subunit f, mitochondrial / type: protein_or_peptide / ID: 12 / Details: ACANB14194 / Number of copies: 1 / 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 #13: ACANB14707

MacromoleculeName: ACANB14707 / type: protein_or_peptide / ID: 13 / Details: ACANB14707 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 10.217619 KDa
SequenceString:
MSKRLITRAT LNGRLATAWA PSRSYAEAAV PKLGKDIQPK NYRRPDGTYE PCDEILFLSV IGYGEDLRAV TNAKEGITNT LVLSRYNKT ASQ

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Macromolecule #14: ATP synthase subunit 9, mitochondrial

MacromoleculeName: ATP synthase subunit 9, mitochondrial / type: protein_or_peptide / ID: 14 / Details: ACANB15917 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 8.249944 KDa
SequenceString:
MKNLEIILQS SKMIGSGLAT SGLIGAGAGV GIVFGCLILA FSRNPNLQKE LFSYALIGFA LTEAIGLLAL VMAFLILFI

UniProtKB: ATP synthase subunit 9, mitochondrial

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Macromolecule #15: ACANB04460

MacromoleculeName: ACANB04460 / type: protein_or_peptide / ID: 15 / Details: ACANB04460 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 15.561524 KDa
SequenceString:
NWSTQLSGNL DALVKRELVD ALAALSAEVK EIDALDQQAK KAHEELLQKL QADIDILTNK ELFAKSLESS GMSPLHVAQM TDIVTTDPL AVQALPLAQK QAAELAQFRQ QSATFQQYSQ LVADSRELVK QLQASGLQFD ASK

UniProtKB: Uncharacterized protein

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Macromolecule #16: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 16 / 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 #17: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 17 / 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

+
Macromolecule #18: unknown protein

MacromoleculeName: unknown protein / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 6.060462 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #19: unknown protein

MacromoleculeName: unknown protein / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 11.251861 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)

+
Macromolecule #20: unknown protein

MacromoleculeName: unknown protein / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 783.958 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #21: unknown protein

MacromoleculeName: unknown protein / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff
Molecular weightTheoretical: 1.635006 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

+
Macromolecule #22: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 22 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #23: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 23 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #24: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 24 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.25 mg/mL
BufferpH: 7.9
Component:
ConcentrationName
50.0 mMHEPES
300.0 mMsodium chloride
4.0 mMMagnesium Chloride
20.0 mMCalcium 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.

-
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: BRIGHT 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

+
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: 4.3 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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