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- EMDB-45038: Cryo-EM structure of ATP synthase non-stator state -

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Basic information

Entry
Database: EMDB / ID: EMD-45038
TitleCryo-EM structure of ATP synthase non-stator state
Map data
Sample
  • Complex: Cryo-EM structure of ATP synthase non-stator state
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATPase inhibitor, mitochondrial
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase F1 subunit delta
    • Protein or peptide: ATP synthase F1 subunit epsilon
    • Protein or peptide: ATP synthase lipid-binding protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsheart / ATP synthase / MEMBRANE PROTEIN
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex binding / regulation of protein targeting to mitochondrion / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / mitochondrial depolarization / ATPase inhibitor activity / positive regulation of type 2 mitophagy / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...mitochondrial proton-transporting ATP synthase complex binding / regulation of protein targeting to mitochondrion / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / mitochondrial depolarization / ATPase inhibitor activity / positive regulation of type 2 mitophagy / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / heme biosynthetic process / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / reactive oxygen species metabolic process / erythrocyte differentiation / ATPase binding / calmodulin binding / mitochondrial inner membrane / intracellular membrane-bounded organelle / lipid binding / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal ...Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / 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, 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, 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 / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain 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 subunit delta, mitochondrial / ATP synthase subunit gamma / ATP synthase subunit beta / ATP synthase F1 subunit epsilon / ATP synthase lipid-binding protein / ATP synthase subunit alpha / ATPase inhibitor, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsZhang Z / Maharjan R / Tringides M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of ATP synthase non-stator state
Authors: Zhang Z / Maharjan R / Tringides M
History
DepositionMay 23, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45038.png

Downloads & links

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Map

FileDownload / File: emd_45038.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.30054083 - 1.1783404
Average (Standard dev.)0.008470523 (±0.027224496)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 547.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of ATP synthase non-stator state

EntireName: Cryo-EM structure of ATP synthase non-stator state
Components
  • Complex: Cryo-EM structure of ATP synthase non-stator state
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATPase inhibitor, mitochondrial
    • Protein or peptide: ATP synthase subunit gamma
    • Protein or peptide: ATP synthase F1 subunit delta
    • Protein or peptide: ATP synthase F1 subunit epsilon
    • Protein or peptide: ATP synthase lipid-binding protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of ATP synthase non-stator state

SupramoleculeName: Cryo-EM structure of ATP synthase non-stator state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 59.502258 KDa
SequenceString: MISGPLKIMT ADLLKGMVSK NALGSSFVAA RNLHASNTRL QKTGTAEVSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQA EEMVEFSSGL KGMSLNLEPD NVGVVVFGND KLIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG P IGSKTRRR ...String:
MISGPLKIMT ADLLKGMVSK NALGSSFVAA RNLHASNTRL QKTGTAEVSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQA EEMVEFSSGL KGMSLNLEPD NVGVVVFGND KLIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG P IGSKTRRR VGLKAPGIIP RISVREPMQT GIKAVDSLVP IGRGQRELII GDRQTGKTSI AIDTIINQKR FNDGTDEKKK LY CIYVAIG QKRSTVAQLV KRLTDADAMK YTIVVSATAS DAAPLQYLAP YSGCSMGEYF RDNGKHALII YDDLSKQAVA YRQ MSLLLR RPPGREAYPG DVFYLHSRLL ERAAKMNDAF GGGSLTALPV IETQAGDVSA YIPTNVISIT DGQIFLETEL FYKG IRPAI NVGLSVSRVG SAAQTRAMKQ VAGTMKLELA QYREVAAFAQ FGSDLDAATQ QLLSRGVRLT ELLKQGQYAP MAIEE QVAV IYAGVRGYLD KLEPSKITKF ENAFLSHVIS QHQALLGKIR ADGKISEETD AKLKEIVTNF LAGFEA

UniProtKB: ATP synthase subunit alpha

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Macromolecule #2: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 60.893625 KDa
SequenceString: MLRVISSKMI QRTCLLQSRP RPQLRGVGGQ TAAALSLYPG SAMLGFVGRV ASASASGALR GLSPSAPLPQ AQLLLRAAPA ALQPARDYA TQPSPSPKAG AATGRIVAVI GAVVDVQFDE GLPPILNALE VQGRETRLVL EVAQHLGEST VRTIAMDGTE G LVRGQKVL ...String:
MLRVISSKMI QRTCLLQSRP RPQLRGVGGQ TAAALSLYPG SAMLGFVGRV ASASASGALR GLSPSAPLPQ AQLLLRAAPA ALQPARDYA TQPSPSPKAG AATGRIVAVI GAVVDVQFDE GLPPILNALE VQGRETRLVL EVAQHLGEST VRTIAMDGTE G LVRGQKVL DSGAPIKIPV GPETLGRIMN VIGEPIDERG PIKTKQFAAI HAEAPEFMEM SVEQEILVTG IKVVDLLAPY AK GGKIGLF GGAGVGKTVL IMELINNVAK AHGGYSVFAG VGERTREGND LYHEMIESGV INLKDATSKV ALVYGQMNEP PGA RARVAL TGLTVAEYFR DQEGQDVLLF IDNIFRFTQA GSEVSALLGR IPSAVGYQPT LATDMGTMQE RITTTKKGSI TSVQ AIYVP ADDLTDPAPA TTFAHLDATT VLSRAIAELG IYPAVDPLDS TSRIMDPNIV GSEHYDVARG VQKILQDYKS LQDII AILG MDELSEEDKL TVSRARKIQR FLSQPFQVAE VFTGHLGKLV PLKETIKGFQ QILAGEYDHL PEQAFYMVGP IEEAVA KAD KLAEEHS

UniProtKB: ATP synthase subunit beta

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Macromolecule #3: ATPase inhibitor, mitochondrial

MacromoleculeName: ATPase inhibitor, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 12.209655 KDa
SequenceString:
MAATALAVRS RIGAWSVWAM QSRGFSSDTP EGVRSGAGAV RDAGGAFGKK EQADEERYFR ARAREQLAAL KKHHENEISH HVKEIERLQ KEIERHKQSI KKLKNDDDD

UniProtKB: ATPase inhibitor, mitochondrial

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Macromolecule #4: ATP synthase subunit gamma

MacromoleculeName: ATP synthase subunit gamma / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 30.252846 KDa
SequenceString: MATLKDITRR LKSIKNIQKI TKSMKMVAAA KYARAERDLK PARVYGIGSL ALYEKADIKV PEDKKKHLII GVSSDRGLCG AIHSSVAKQ IKSEVANLTA AGKEVKIVGV GDKIRGILHR THSDQFLVTF KEVGRKPPTF GDASVIALEL LNSGYEFDEG S IIFNRFRS ...String:
MATLKDITRR LKSIKNIQKI TKSMKMVAAA KYARAERDLK PARVYGIGSL ALYEKADIKV PEDKKKHLII GVSSDRGLCG AIHSSVAKQ IKSEVANLTA AGKEVKIVGV GDKIRGILHR THSDQFLVTF KEVGRKPPTF GDASVIALEL LNSGYEFDEG S IIFNRFRS VISYKTEEKP IFSLDTVASA ESMSIYDDID ADVLRNYQEY SLANIIYYSL KESTTSEQSA RMTAMDNASK NA SEMIDKL TLTFNRTRQA VITKELIEII SGAAAL

UniProtKB: ATP synthase subunit gamma

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Macromolecule #5: ATP synthase F1 subunit delta

MacromoleculeName: ATP synthase F1 subunit delta / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 17.489729 KDa
SequenceString:
MLPATLLRRS GLGRVVRQAR AYAEAAAAPA SAAGPGQMSF TFASPTQVFF NGANVRQVDV PTQTGAFGIL ASHVPTLQVL RPGLVVVHA EDGTTSKYFV SSGSVTVNAD SSVQLLAEEA VTLDMLDPGV AKANLEKAQS ELLGAADEAS RAEIQIRIEA N EALVKALE

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

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Macromolecule #6: ATP synthase F1 subunit epsilon

MacromoleculeName: ATP synthase F1 subunit epsilon / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 14.774812 KDa
SequenceString:
FPFNNCREQT NSLNCLGLQA APRWTGAEGL RPLLPGLSLG THPGLSRTSA ACHGVGSPRP SWAARSEPTL TGPRDSTRRA HSSDIMVAY WRQAGLSYIR YSQICAKAVR DALKAEFKAN AEKTSGSNVK IVKVKKE

UniProtKB: ATP synthase F1 subunit epsilon

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Macromolecule #7: ATP synthase lipid-binding protein

MacromoleculeName: ATP synthase lipid-binding protein / type: protein_or_peptide / ID: 7 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 14.596909 KDa
SequenceString:
MFACTKLACT PALIRAGSRV AYRPISASVL SRPEARPGEG STVFNGAQNG VSQPIQREFQ TSAVSRDIDT AAKFIGAGAA TVGVAGSGA GIGTVFGSLI IGYARNPSLK QQLFSYAILG FALSEAMGLF CLMVAFLILF AM

UniProtKB: ATP synthase lipid-binding protein

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Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / 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 #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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 / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19085
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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