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- EMDB-65237: IF1 bound bovine F-ATP synthase planar dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-65237
TitleIF1 bound bovine F-ATP synthase planar dimer
Map dataIF1 bound planar dimer of bovine F-ATP synthase.
Sample
  • Complex: Bovine F-ATP synthase in the oligomeric form of an IF1 bound planar dimer
    • Protein or peptide: x 16 types
KeywordsATP synthase/hydrolase / oligomer / membrane bending / mammalian mitochondria / MEMBRANE PROTEIN
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsNakano A / Jiko C / Yamashita E / Yokoyama K / Gerle C
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22ama 121003 Japan
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
CitationJournal: Biorxiv / Year: 2025
Title: A planar dimer of bovine ATP synthase
Authors: Jiko C / Nakano A / Teshirogi Y / Yamashita E / Kurisu G / Standley D / Terada T / Mitsuoka K / Yokoyama K / Gerle C
History
DepositionJul 3, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65237.png

Downloads & links

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Map

FileDownload / File: emd_65237.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIF1 bound planar dimer of bovine F-ATP synthase.
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 250 pix.
= 546. Å		2.18 Å/pix.
x 250 pix.
= 546. Å		2.18 Å/pix.
x 250 pix.
= 546. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.184 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.555
Minimum - Maximum-0.58849114 - 2.1802971
Average (Standard dev.)0.0025088058 (±0.0953743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 546.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65237_msk_1.map
Projections & Slices
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Histogram

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Half map: half map B

Fileemd_65237_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_65237_half_map_2.map
Annotationhalf map A
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Bovine F-ATP synthase in the oligomeric form of an IF1 bound plan...

EntireName: Bovine F-ATP synthase in the oligomeric form of an IF1 bound planar dimer
Components
  • Complex: Bovine F-ATP synthase in the oligomeric form of an IF1 bound planar dimer
    • Protein or peptide: ATP synthase F(0) complex subunit 8
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
    • Protein or peptide: ATP synthase F(1) complex subunit gamma, mitochondrial
    • Protein or peptide: ATP synthase F(1) complex subunit delta, mitochondrial
    • Protein or peptide: ATP synthase F(1) complex subunit epsilon, mitochondrial
    • Protein or peptide: ATPase inhibitor, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit C2, mitochondrial
    • Protein or peptide: ATP synthase peripheral stalk subunit OSCP, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit a
    • Protein or peptide: ATP synthase peripheral stalk subunit b, mitochondrial
    • Protein or peptide: ATP synthase peripheral stalk subunit d, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit e, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit f, mitochondrial
    • Protein or peptide: ATP synthase F(0) complex subunit g, mitochondrial
    • Protein or peptide: ATP synthase peripheral stalk subunit F6, mitochondrial

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Supramolecule #1: Bovine F-ATP synthase in the oligomeric form of an IF1 bound plan...

SupramoleculeName: Bovine F-ATP synthase in the oligomeric form of an IF1 bound planar dimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Oligomer fractions of bovine F-ATP synthase obtained from heart muscle tissue mitochondria.
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: heart / Tissue: muscle / Organelle: mitochondria
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: ATP synthase F(0) complex subunit 8

MacromoleculeName: ATP synthase F(0) complex subunit 8 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.944523 KDa
SequenceString:
MPQLDTSTWL TMILSMFLTL FIIFQLKVSK HNFYHNPELT PTKMLKQNTP WETKWTKIYL PLLLPL

UniProtKB: ATP synthase F(0) complex subunit 8

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Macromolecule #2: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 59.765469 KDa
SequenceString: MLSVRVAAAV ARALPRRAGL VSKNALGSSF IAARNLHASN SRLQKTGTAE VSSILEERIL GADTSVDLEE TGRVLSIGDG IARVHGLRN VQAEEMVEFS SGLKGMSLNL EPDNVGVVVF GNDKLIKEGD IVKRTGAIVD VPVGEELLGR VVDALGNAID G KGPIGSKA ...String:
MLSVRVAAAV ARALPRRAGL VSKNALGSSF IAARNLHASN SRLQKTGTAE VSSILEERIL GADTSVDLEE TGRVLSIGDG IARVHGLRN VQAEEMVEFS SGLKGMSLNL EPDNVGVVVF GNDKLIKEGD IVKRTGAIVD VPVGEELLGR VVDALGNAID G KGPIGSKA RRRVGLKAPG IIPRISVREP MQTGIKAVDS LVPIGRGQRE LIIGDRQTGK TSIAIDTIIN QKRFNDGTDE KK KLYCIYV AIGQKRSTVA QLVKRLTDAD AMKYTIVVSA TASDAAPLQY LAPYSGCSMG EYFRDNGKHA LIIYDDLSKQ AVA YRQMSL LLRRPPGREA YPGDVFYLHS RLLERAAKMN DAFGGGSLTA LPVIETQAGD VSAYIPTNVI SITDGQIFLE TELF YKGIR PAINVGLSVS RVGSAAQTRA MKQVAGTMKL ELAQYREVAA FAQFGSDLDA ATQQLLSRGV RLTELLKQGQ YSPMA IEEQ VAVIYAGVRG YLDKLEPSKI TKFENAFLSH VISQHQALLG KIRTDGKISE ESDAKLKEIV TNFLAGFEA

UniProtKB: ATP synthase subunit alpha

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Macromolecule #3: ATP synthase F(1) complex catalytic subunit beta, mitochondrial

MacromoleculeName: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 56.340199 KDa
SequenceString: MLGLVGRVVA ASASGALRGL SPSAPLPQAQ LLLRAAPAAL QPARDYAAQA SPSPKAGATT GRIVAVIGAV VDVQFDEGLP PILNALEVQ GRETRLVLEV AQHLGESTVR TIAMDGTEGL VRGQKVLDSG APIRIPVGPE TLGRIMNVIG EPIDERGPIK T KQFAAIHA ...String:
MLGLVGRVVA ASASGALRGL SPSAPLPQAQ LLLRAAPAAL QPARDYAAQA SPSPKAGATT GRIVAVIGAV VDVQFDEGLP PILNALEVQ GRETRLVLEV AQHLGESTVR TIAMDGTEGL VRGQKVLDSG APIRIPVGPE TLGRIMNVIG EPIDERGPIK T KQFAAIHA EAPEFVEMSV EQEILVTGIK VVDLLAPYAK GGKIGLFGGA GVGKTVLIME LINNVAKAHG GYSVFAGVGE RT REGNDLY HEMIESGVIN LKDATSKVAL VYGQMNEPPG ARARVALTGL TVAEYFRDQE GQDVLLFIDN IFRFTQAGSE VSA LLGRIP SAVGYQPTLA TDMGTMQERI TTTKKGSITS VQAIYVPADD LTDPAPATTF AHLDATTVLS RAIAELGIYP AVDP LDSTS RIMDPNIVGS EHYDVARGVQ KILQDYKSLQ DIIAILGMDE LSEEDKLTVS RARKIQRFLS QPFQVAEVFT GHLGK LVPL KETIKGFQQI LAGEYDHLPE QAFYMVGPIE EAVAKADKLA EEHS

UniProtKB: ATP synthase F(1) complex catalytic subunit beta, mitochondrial

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Macromolecule #4: ATP synthase F(1) complex subunit gamma, mitochondrial

MacromoleculeName: ATP synthase F(1) complex subunit gamma, mitochondrial
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 33.119035 KDa
SequenceString: MFSRAGVAGL SAWTVQPQWI QVRNMATLKD ITRRLKSIKN IQKITKSMKM VAAAKYARAE RELKPARVYG VGSLALYEKA DIKTPEDKK KHLIIGVSSD RGLCGAIHSS VAKQMKSEAA NLAAAGKEVK IIGVGDKIRS ILHRTHSDQF LVTFKEVGRR P PTFGDASV ...String:
MFSRAGVAGL SAWTVQPQWI QVRNMATLKD ITRRLKSIKN IQKITKSMKM VAAAKYARAE RELKPARVYG VGSLALYEKA DIKTPEDKK KHLIIGVSSD RGLCGAIHSS VAKQMKSEAA NLAAAGKEVK IIGVGDKIRS ILHRTHSDQF LVTFKEVGRR P PTFGDASV IALELLNSGY EFDEGSIIFN RFRSVISYKT EEKPIFSLDT ISSAESMSIY DDIDADVLRN YQEYSLANII YY SLKESTT SEQSARMTAM DNASKNASEM IDKLTLTFNR TRQAVITKEL IEIISGAAAL D

UniProtKB: ATP synthase F(1) complex subunit gamma, mitochondrial

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Macromolecule #5: ATP synthase F(1) complex subunit delta, mitochondrial

MacromoleculeName: ATP synthase F(1) complex subunit delta, mitochondrial
type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 17.626992 KDa
SequenceString:
MLPSALLRRP GLGRLVRQVR LYAEAAAAQA PAAGPGQMSF TFASPTQVFF NSANVRQVDV PTQTGAFGIL AAHVPTLQVL RPGLVVVHA EDGTTSKYFV SSGSVTVNAD SSVQLLAEEA VTLDMLDLGA AKANLEKAQS ELLGAADEAT RAEIQIRIEA N EALVKALE

UniProtKB: ATP synthase F(1) complex subunit delta, mitochondrial

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Macromolecule #6: ATP synthase F(1) complex subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase F(1) complex subunit epsilon, mitochondrial
type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 5.793889 KDa
SequenceString:
MVAYWRQAGL SYIRYSQICA KAVRDALKTE FKANAMKTSG STIKIVKVKK E

UniProtKB: ATP synthase F(1) complex subunit epsilon, mitochondrial

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Macromolecule #7: ATPase inhibitor, mitochondrial

MacromoleculeName: ATPase inhibitor, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: heart / Tissue: muscle
Molecular weightTheoretical: 12.326715 KDa
SequenceString:
MAATALAART RQAVWSVWAM QGRGFGSESG DNVRSSAGAV RDAGGAFGKR EQAEEERYFR ARAKEQLAAL KKHHENEISH HAKEIERLQ KEIERHKQSI KKLKQSEDDD

UniProtKB: ATPase inhibitor, mitochondrial

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Macromolecule #8: ATP synthase F(0) complex subunit C2, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit C2, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 15.041492 KDa
SequenceString:
MYTCAKFVST PSLIRRTSTV LSRSLSAVVV RRPETLTDES HSSLAVVPRP LTTSLTPSRS FQTSAISRDI DTAAKFIGAG AATVGVAGS GAGIGTVFGS LIIGYARNPS LKQQLFSYAI LGFALSEAMG LFCLMVAFLI LFAM

UniProtKB: ATP synthase F(0) complex subunit C2, mitochondrial

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Macromolecule #9: ATP synthase peripheral stalk subunit OSCP, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit OSCP, mitochondrial
type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 23.351596 KDa
SequenceString: MAALAVSGLS QQVRCFSTSV VRPFAKLVRP PVQIYGIEGR YATALYSAAS KQNKLEQVEK ELLRVGQILK EPKMAASLLN PYVKRSVKV KSLSDMTAKE KFSPLTSNLI NLLAENGRLT NTPAVISAFS TMMSVHRGEV PCTVTTASAL DEATLTELKT V LKSFLSKG ...String:
MAALAVSGLS QQVRCFSTSV VRPFAKLVRP PVQIYGIEGR YATALYSAAS KQNKLEQVEK ELLRVGQILK EPKMAASLLN PYVKRSVKV KSLSDMTAKE KFSPLTSNLI NLLAENGRLT NTPAVISAFS TMMSVHRGEV PCTVTTASAL DEATLTELKT V LKSFLSKG QVLKLEVKID PSIMGGMIVR IGEKYVDMSA KTKIQKLSRA MREIL

UniProtKB: ATP synthase peripheral stalk subunit OSCP, mitochondrial

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Macromolecule #10: ATP synthase F(0) complex subunit a

MacromoleculeName: ATP synthase F(0) complex subunit a / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 24.801785 KDa
SequenceString: MNENLFTSFI TPVILGLPLV TLIVLFPSLL FPTSNRLVSN RFVTLQQWML QLVSKQMMSI HNSKGQTWTL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW AGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPMALAVR L TANITAGH ...String:
MNENLFTSFI TPVILGLPLV TLIVLFPSLL FPTSNRLVSN RFVTLQQWML QLVSKQMMSI HNSKGQTWTL MLMSLILFIG STNLLGLLP HSFTPTTQLS MNLGMAIPLW AGAVITGFRN KTKASLAHFL PQGTPTPLIP MLVIIETISL FIQPMALAVR L TANITAGH LLIHLIGGAT LALMSISTTT ALITFTILIL LTILEFAVAM IQAYVFTLLV SLYLHDNT

UniProtKB: ATP synthase F(0) complex subunit a

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Macromolecule #11: ATP synthase peripheral stalk subunit b, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit b, mitochondrial
type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 28.859629 KDa
SequenceString: MLSRVVLSAA AAAAPSLKNA ALLGPGVLQA TRIFHTGQPS LAPVPPLPEH GGKVRFGLIP EEFFQFLYPK TGVTGPYVLG TGLILYLLS KEIYVITPET FSAISTIGFL VYIVKKYGAS VGEFADKLNE QKIAQLEEVK QASIKQIQDA IDMEKSQQAL V QKRHYLFD ...String:
MLSRVVLSAA AAAAPSLKNA ALLGPGVLQA TRIFHTGQPS LAPVPPLPEH GGKVRFGLIP EEFFQFLYPK TGVTGPYVLG TGLILYLLS KEIYVITPET FSAISTIGFL VYIVKKYGAS VGEFADKLNE QKIAQLEEVK QASIKQIQDA IDMEKSQQAL V QKRHYLFD VQRNNIAMAL EVTYRERLHR VYREVKNRLD YHISVQNMMR QKEQEHMINW VEKRVVQSIS AQQEKETIAK CI ADLKLLS KKAQAQPVM

UniProtKB: ATP synthase peripheral stalk subunit b, mitochondrial

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Macromolecule #12: ATP synthase peripheral stalk subunit d, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit d, mitochondrial
type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 18.719453 KDa
SequenceString:
MAGRKLALKT IDWVAFGEII PRNQKAVANS LKSWNETLTS RLATLPEKPP AIDWAYYKAN VAKAGLVDDF EKKFNALKVP IPEDKYTAQ VDAEEKEDVK SCAEFLTQSK TRIQEYEKEL EKMRNIIPFD QMTIEDLNEV FPETKLDKKK YPYWPHRPIE T L

UniProtKB: ATP synthase peripheral stalk subunit d, mitochondrial

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Macromolecule #13: ATP synthase F(0) complex subunit e, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit e, mitochondrial / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 8.336688 KDa
SequenceString:
MVPPVQVSPL IKLGRYSALF LGMAYGAKRY NYLKPRAEEE RRLAAEEKKK RDEQKRIERE LAEAQEDTIL K

UniProtKB: ATP synthase F(0) complex subunit e, mitochondrial

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Macromolecule #14: ATP synthase F(0) complex subunit f, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit f, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 10.315207 KDa
SequenceString:
MASVVPLKEK KLLEVKLGEL PSWILMRDFT PSGIAGAFQR GYYRYYNKYV NVKKGSIAGL SMVLAAYVFL NYCRSYKELK HERLRKYH

UniProtKB: ATP synthase F(0) complex subunit f, mitochondrial

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Macromolecule #15: ATP synthase F(0) complex subunit g, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit g, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 11.429393 KDa
SequenceString:
MAEFVRNLAE KAPALVNAAV TYSKPRLATF WYYAKVELVP PTPAEIPTAI QSLKKIINSA KTGSFKQLTV KEALLNGLVA TEVWMWFYV GEIIGKRGII GYDV

UniProtKB: ATP synthase F(0) complex subunit g, mitochondrial

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Macromolecule #16: ATP synthase peripheral stalk subunit F6, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit F6, mitochondrial
type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 12.549321 KDa
SequenceString:
MILQRLFRLS SAVQSAISVS WRRNIGITAV AFNKELDPVQ KLFVDKIREY RTKRQTSGGP VDAGPEYQQD LDRELFKLKQ MYGKADMNT FPNFTFEDPK FEVVEKPQS

UniProtKB: ATP synthase peripheral stalk subunit F6, mitochondrial

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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

Concentration5 mg/mL
BufferpH: 7.3
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
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: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 22478
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6ziu

source_name: PDB, initial_model_type: experimental model

6z1u

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9vpb:
Cryo-EM structure of the IF1 bound bovine F-ATP synthase planar dimer

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