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- EMDB-65239: IF1 bound bovine ATP synthase monomer: rotary state 1, F1 focused map -

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Basic information

Entry
Database: EMDB / ID: EMD-65239
TitleIF1 bound bovine ATP synthase monomer: rotary state 1, F1 focused map
Map dataF1 focused map of the state 1 bovine ATP synthase monomer.
Sample
  • Complex: IF1 bound bovine ATP synthase monomer isolated from heart muscle tissue mitochondria
    • Protein or peptide: x 10 types
  • Ligand: x 4 types
KeywordsATP synthase/hydrolase / oligomer / membrane bending / mammalian mitochondria / membrane protein / motor protein
Function / homology
Function and homology information


negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation ...negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / heme biosynthetic process / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / erythrocyte differentiation / aerobic respiration / ADP binding / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) ...Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / 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, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / 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, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / 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 F(1) complex catalytic subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 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)JP22ama121003 Japan
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
Citation
Journal: Cell Death Differ / Year: 2026
Title: A planar dimer of bovine ATP synthase.
Authors: Chimari Jiko / Atsuki Nakano / Yosuke Teshirogi / Eiki Yamashita / Genji Kurisu / Daron Standley / Tohru Terada / Kaoru Mitsuoka / Ken Yokoyama / Christoph Gerle /
Abstract: Mammalian mitochondrial ATP synthase typically organizes into rows of V-shaped dimers that impose significant membrane curvature essential for mitochondrial cristae formation. Using gentle, column- ...Mammalian mitochondrial ATP synthase typically organizes into rows of V-shaped dimers that impose significant membrane curvature essential for mitochondrial cristae formation. Using gentle, column-free purification combined with single-particle cryo-electron microscopy, we have identified a previously unrecognized planar dimeric form of bovine ATP synthase exhibiting minimal membrane bending. This planar dimer is characterized structurally by anti-parallel arrangement of two ATP synthase complexes linked by a straight conformation of inhibitory factor 1 (IF1), a sharp contrast to the kinked IF1 observed in tetrameric assemblies. Molecular dynamics simulations confirm that transitioning between straight and kinked IF1 conformations occurs without significant energetic barriers. The planar dimer also displays distinct peripheral stalk positioning relative to its adjacent α subunit. These structural divergences suggest a specialized function and a distinct localization for planar ATP synthase dimers, providing structural support for a division of labor within mitochondrial ATP synthase populations.
#1: Journal: 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 15, 2026-
Current statusJul 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65239.png

Downloads & links

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Map

FileDownload / File: emd_65239.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationF1 focused map of the state 1 bovine ATP synthase monomer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 340 pix.
= 319.199 Å		0.94 Å/pix.
x 340 pix.
= 319.199 Å		0.94 Å/pix.
x 340 pix.
= 319.199 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93882 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.38729236 - 1.2142338
Average (Standard dev.)0.0005502566 (±0.031140687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 319.1988 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65239_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_65239_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_65239_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 : IF1 bound bovine ATP synthase monomer isolated from heart muscle ...

EntireName: IF1 bound bovine ATP synthase monomer isolated from heart muscle tissue mitochondria
Components
  • Complex: IF1 bound bovine ATP synthase monomer isolated from heart muscle tissue mitochondria
    • Protein or peptide: ATP synthase F(1) complex subunit alpha, mitochondrial
    • 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 peripheral stalk subunit OSCP, mitochondrial
    • 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 peripheral stalk subunit F6, mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water

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Supramolecule #1: IF1 bound bovine ATP synthase monomer isolated from heart muscle ...

SupramoleculeName: IF1 bound bovine ATP synthase monomer isolated from heart muscle tissue mitochondria
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 600 KDa

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

MacromoleculeName: ATP synthase F(1) complex subunit alpha, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 59.795492 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 VISQHQALLS KIRTDGKISE ESDAKLKEIV TNFLAGFEA

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

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Macromolecule #2: ATP synthase F(1) complex catalytic subunit beta, mitochondrial

MacromoleculeName: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 3 / 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 #3: ATP synthase F(1) complex subunit gamma, mitochondrial

MacromoleculeName: ATP synthase F(1) complex subunit gamma, mitochondrial
type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #4: ATP synthase F(1) complex subunit delta, mitochondrial

MacromoleculeName: ATP synthase F(1) complex subunit delta, mitochondrial
type: protein_or_peptide / ID: 4 / Number of copies: 1 / 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 #5: ATP synthase F(1) complex subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase F(1) complex subunit epsilon, mitochondrial
type: protein_or_peptide / ID: 5 / Number of copies: 1 / 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 #6: ATPase inhibitor, mitochondrial

MacromoleculeName: ATPase inhibitor, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
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 #7: ATP synthase peripheral stalk subunit OSCP, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit OSCP, mitochondrial
type: protein_or_peptide / ID: 7 / Number of copies: 1 / 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 #8: ATP synthase peripheral stalk subunit b, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit b, mitochondrial
type: protein_or_peptide / ID: 8 / Number of copies: 1 / 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 #9: ATP synthase peripheral stalk subunit d, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit d, mitochondrial
type: protein_or_peptide / ID: 9 / Number of copies: 1 / 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 #10: ATP synthase peripheral stalk subunit F6, mitochondrial

MacromoleculeName: ATP synthase peripheral stalk subunit F6, mitochondrial
type: protein_or_peptide / ID: 10 / Number of copies: 1 / 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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Macromolecule #11: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 11 / 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 #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #14: water

MacromoleculeName: water / type: ligand / ID: 14 / Number of copies: 17 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration4.0 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 / 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: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 398620
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6yy0


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9vpd:
Cryo-EM structure of the IF1 bound bovine ATP synthase monomer: rotary state 1, F1 focused map

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