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- EMDB-44776: Artemia franciscana ATP synthase FO domain, state 1, pH 7.0 -

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Entry
Database: EMDB / ID: EMD-44776
TitleArtemia franciscana ATP synthase FO domain, state 1, pH 7.0
Map dataArtemia franciscana ATP synthase FO domain, state 1, pH 7.0
Sample
  • Complex: Mitochondrial ATP synthase
    • Protein or peptide: x 12 types
  • Ligand: x 1 types
KeywordsATP synthesis / Complex V / mitochondria / oxidative-phosphorylation / MEMBRANE PROTEIN
Function / homology
Function and homology information


ATP biosynthetic process / proton-transporting ATP synthase complex / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / : / : / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / mitochondrial membrane / mitochondrial inner membrane
Similarity search - Function
ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / 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, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / 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. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase
Similarity search - Domain/homology
ATP synthase subunit e, mitochondrial / ATP synthase subunit gamma / ATP synthase subunit / ATP synthase protein 8 / ATP synthase subunit a
Similarity search - Component
Biological speciesArtemia franciscana (crustacean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMnatsakanyan N / Mello JFR
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG072484 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS137275 United States
CitationJournal: Cell Death Differ / Year: 2025
Title: Cryo-EM structure of the brine shrimp mitochondrial ATP synthase suggests an inactivation mechanism for the ATP synthase leak channel.
Authors: Amrendra Kumar / Juliana da Fonseca Rezende E Mello / Yangyu Wu / Daniel Morris / Ikram Mezghani / Erin Smith / Stephane Rombauts / Peter Bossier / Juno Krahn / Fred J Sigworth / Nelli Mnatsakanyan /
Abstract: Mammalian mitochondria undergo Ca-induced and cyclosporinA (CsA)-regulated permeability transition (mPT) by activating the mitochondrial permeability transition pore (mPTP) situated in mitochondrial ...Mammalian mitochondria undergo Ca-induced and cyclosporinA (CsA)-regulated permeability transition (mPT) by activating the mitochondrial permeability transition pore (mPTP) situated in mitochondrial inner membranes. Ca-induced prolonged openings of mPTP under certain pathological conditions result in mitochondrial swelling and rupture of the outer membrane, leading to mitochondrial dysfunction and cell death. While the exact molecular composition and structure of mPTP remain unknown, mammalian ATP synthase was reported to form voltage and Ca-activated leak channels involved in mPT. Unlike in mammals, mitochondria of the crustacean Artemia franciscana have the ability to accumulate large amounts of Ca without undergoing the mPT. Here, we performed structural and functional analysis of A. franciscana ATP synthase to study the molecular mechanism of mPTP inhibition in this organism. We found that the channel formed by the A. franciscana ATP synthase dwells predominantly in its inactive state and is insensitive to Ca, in contrast to porcine heart ATP synthase. Single-particle cryo-electron microscopy (cryo-EM) analysis revealed distinct structural features in A. franciscana ATP synthase compared with mammals. The stronger density of the e-subunit C-terminal region and its enhanced interaction with the c-ring were found in A. franciscana ATP synthase. These data suggest an inactivation mechanism of the ATP synthase leak channel and its possible contribution to the lack of mPT in this organism.
History
DepositionMay 7, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44776.png

Downloads & links

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Map

FileDownload / File: emd_44776.map.gz / Format: CCP4 / Size: 5.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationArtemia franciscana ATP synthase FO domain, state 1, pH 7.0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 97 pix.
= 103.596 Å		1.07 Å/pix.
x 112 pix.
= 119.616 Å		1.07 Å/pix.
x 141 pix.
= 150.588 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.234
Minimum - Maximum-1.321581 - 2.1500223
Average (Standard dev.)0.043174002 (±0.14963159)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin211241218
Dimensions11214197
Spacing97112141
CellA: 103.59599 Å / B: 119.616 Å / C: 150.588 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Artemia franciscana ATP synthase FO domain, state 1, pH 7.0

Fileemd_44776_half_map_1.map
AnnotationArtemia franciscana ATP synthase FO domain, state 1, pH 7.0
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Artemia franciscana ATP synthase FO domain, state 1, pH 7.0

Fileemd_44776_half_map_2.map
AnnotationArtemia franciscana ATP synthase FO domain, state 1, pH 7.0
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial ATP synthase

EntireName: Mitochondrial ATP synthase
Components
  • Complex: Mitochondrial ATP synthase
    • Protein or peptide: ATP synthase subunit c
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase subunit delta
    • Protein or peptide: ATP synthase subunit epsilon
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit d
    • Protein or peptide: ATP synthase subunit a
    • Protein or peptide: ATP synthase subunit 6.8PL
    • Protein or peptide: ATP synthase protein 8
    • Protein or peptide: ATP synthase subunit f
    • Protein or peptide: ATP synthase subunit g
    • Protein or peptide: ATP synthase subunit e
  • Ligand: CARDIOLIPIN

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Supramolecule #1: Mitochondrial ATP synthase

SupramoleculeName: Mitochondrial ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Artemia franciscana (crustacean)

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Macromolecule #1: ATP synthase subunit c

MacromoleculeName: ATP synthase subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 13.250408 KDa
SequenceString:
MYTIARIATR AAVSQGSQAY LRPVSSAVLS QKVIVEAPVA TQARSLQTSA VQRDIDSAAK FIGAGAATVG VAGSGAGIGS VFGSLIIGY ARNPSLKQQL FSYAILGFAL SEAMGLFCLM MAFLLLFAF

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Macromolecule #2: ATP synthase subunit gamma

MacromoleculeName: ATP synthase subunit gamma / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 31.976818 KDa
SequenceString: MFGRTSVLVL SQCNAAEQVR GMATLKAVSI RLKSVKNIQK ITQSMKMVSA AKYTKAEREL RVAKPYGQGA MKFYEKTELK GKEEKPSQL IIAISSDRGL CGAVHSSVGR QLKADLAANP DTMVICVGDK IRNILQRLYG NNLAMVCNDF GRRPPVFEDA T KVARAVLE ...String:
MFGRTSVLVL SQCNAAEQVR GMATLKAVSI RLKSVKNIQK ITQSMKMVSA AKYTKAEREL RVAKPYGQGA MKFYEKTELK GKEEKPSQL IIAISSDRGL CGAVHSSVGR QLKADLAANP DTMVICVGDK IRNILQRLYG NNLAMVCNDF GRRPPVFEDA T KVARAVLE SGMEFTNGKI VYNAFRSVVS FRTTDIPVFS KNAIESADSI AAYDSLDSDV IQSYVEYSLA SLIYYTMKEN AT SEQSSRM TAMDNASKNA GEMIDKLTMT FNRTRQAVIT RELIEIISGA SAL

UniProtKB: ATP synthase subunit gamma

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Macromolecule #3: ATP synthase subunit delta

MacromoleculeName: ATP synthase subunit delta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 17.565455 KDa
SequenceString:
MVSLTGDVST VVGPTEVDSA EVGFADVSSA WDNQMAFTFA APSQVFYNNA NIRQVDVPSF SGSFGILPAH VATLAVLKPG VVTVYQEDG STKKYFVSSG TVTVNDDSSV QVLAEEAVPV ENLDLQAARD ILSKAQSDVT SAGADMLKLA EGQIAVEVGE A LVKAAEGQ L

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Macromolecule #4: ATP synthase subunit epsilon

MacromoleculeName: ATP synthase subunit epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 7.464596 KDa
SequenceString:
VRSNFASISG SGRRGRHVDF GASVDFEVHM MRRALKPELR NEAIKREESL LKVTPWKDGK PVKAAQ

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Macromolecule #5: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 29.944416 KDa
SequenceString: MLSRIAVQSA RPIAALQSVR PVQTSSTKTS EVASASVAPV VQFKGPNEGV ERDHVGFPRP LRPVNPGKVR VGFVPEEWFT FFYNKTGVT GPYVLGAGAL TFLLSKEIYV VEHEFYTGVA IAIMGTYGVK KFGKQIADYA DKGIGEIEQS FKEYQDSSKI G FEEAITLE ...String:
MLSRIAVQSA RPIAALQSVR PVQTSSTKTS EVASASVAPV VQFKGPNEGV ERDHVGFPRP LRPVNPGKVR VGFVPEEWFT FFYNKTGVT GPYVLGAGAL TFLLSKEIYV VEHEFYTGVA IAIMGTYGVK KFGKQIADYA DKGIGEIEQS FKEYQDSSKI G FEEAITLE ERAQKSAEAQ IMLFQAKREN VQFQLEAAYR ARLHHVNNEI KKRLDYHLET ERAQRQIKQK NMVDWIVRNV MK SITPEQE RLMLSKCISD LKAMSIKA

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Macromolecule #6: ATP synthase subunit d

MacromoleculeName: ATP synthase subunit d / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 25.422525 KDa
SequenceString: MASKRIARSS IDWAKMAESV PESQKAMYNQ FKAKSDGYIR KALSYPEQPS PINWEHYRKS LTNPAMVDAF KKQYEALKVP YPEDKVSSQ IDAQEAEAKK EITKFIQESR GRIENYKAEL GKLGQMIPFE HMTLEDFFEA FPEKVLNPDP PSPNVKKKPF K NNSWHLIQ ...String:
MASKRIARSS IDWAKMAESV PESQKAMYNQ FKAKSDGYIR KALSYPEQPS PINWEHYRKS LTNPAMVDAF KKQYEALKVP YPEDKVSSQ IDAQEAEAKK EITKFIQESR GRIENYKAEL GKLGQMIPFE HMTLEDFFEA FPEKVLNPDP PSPNVKKKPF K NNSWHLIQ KIPNHFGLIL KKTLWNSKRR NSGNLEMNTI KSILLLDIIF KSFIGIKMCK L

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Macromolecule #7: ATP synthase subunit a

MacromoleculeName: ATP synthase subunit a / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 24.422471 KDa
SequenceString: MMASLFSVFD PTSSFLSNWL SMLIPLLFMV MSFWLIPSRP QFLAKSVLMG LNREMSLLMG PASFGANILV IALFLFILFN NFIGLFPYI FTATSHLAVT LSLAVPLWIS FILYTWIKET TNALAHLVPL GTPAPLMPFM VLMEIISNMI RPITLSVRLA A NMIAGHLL ...String:
MMASLFSVFD PTSSFLSNWL SMLIPLLFMV MSFWLIPSRP QFLAKSVLMG LNREMSLLMG PASFGANILV IALFLFILFN NFIGLFPYI FTATSHLAVT LSLAVPLWIS FILYTWIKET TNALAHLVPL GTPAPLMPFM VLMEIISNMI RPITLSVRLA A NMIAGHLL LTLLGAQGTL ENLYVTSIVV FSQIILLMLE FSVAIIQSYV FMTLMTLYAS E

UniProtKB: ATP synthase subunit a

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Macromolecule #8: ATP synthase subunit 6.8PL

MacromoleculeName: ATP synthase subunit 6.8PL / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 3.762629 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)

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Macromolecule #9: ATP synthase protein 8

MacromoleculeName: ATP synthase protein 8 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 6.351719 KDa
SequenceString:
MPQMMPLPWI MVFLVSMALL WAIMTMVFFL YQPRSVSSAK GFSDRTVYLN WKW

UniProtKB: ATP synthase protein 8

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Macromolecule #10: ATP synthase subunit f

MacromoleculeName: ATP synthase subunit f / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 13.6978 KDa
SequenceString:
MGFGDYPAEY NPKVHGPYDP ARFYGKADVP LGQVKLGELS QWLGRRNKNP QAVAAAVSRG WWRWQHKYVL PRKGGIAPYI QLIVGCSIF FYAINYGKMV AHRQRKYHCR KTHSISHSNI

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Macromolecule #11: ATP synthase subunit g

MacromoleculeName: ATP synthase subunit g / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 11.236328 KDa
SequenceString:
MSALAKKIAT SGPVVLKNTI AVTRPKLATF LKYAKVELTP PGPADVPKIQ EGIQNLIHSA KTGKWKQVSV REAWLNTLIV TEIAMWFFV GECIGKGSVI GYRV

UniProtKB: ATP synthase subunit

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Macromolecule #12: ATP synthase subunit e

MacromoleculeName: ATP synthase subunit e / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Artemia franciscana (crustacean)
Molecular weightTheoretical: 9.557997 KDa
SequenceString:
MSFAPPVNVS PLIRAGRYGA LVVGIVYGSY RFGSLQKREN EWRVEEARRK VIRDALNAEN KAKATREEML YLAKETGVKV PENF

UniProtKB: ATP synthase subunit e, mitochondrial

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Macromolecule #13: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 13 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*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

Concentration0.5 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 15.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 673185
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: integrative model / Details: Genome annotation and Alpha fold
Output model

PDB-9bpg:
Artemia franciscana ATP synthase FO domain, state 1, pH 7.0

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