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- EMDB-25932: Yeast ATP synthase F1 region State 1-3binding beta_tight open wit... -
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Open data
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Basic information
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Title | Yeast ATP synthase F1 region State 1-3binding beta_tight open without exogenous ATP | ||||||||||||
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![]() | F1-ATPase / ATP Synthase / Hydrolase / Nanomotor / Complex | ||||||||||||
Function / homology | ![]() : / : / : / Mitochondrial protein degradation / : / : / mitochondrial nucleoid / : / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) ...: / : / : / Mitochondrial protein degradation / : / : / mitochondrial nucleoid / : / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / proton motive force-driven mitochondrial ATP synthesis / mitochondrial intermembrane space / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Guo H / Rubinstein JL | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of ATP synthase under strain during catalysis. Authors: Hui Guo / John L Rubinstein / ![]() Abstract: ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor ...ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor subcomplex and are held stationary relative to each other by a peripheral stalk. Structures of resting mitochondrial ATP synthases revealed a left-handed curvature of the peripheral stalk even though rotation of the rotor, driven by either ATP hydrolysis in F or proton translocation through F, would apply a right-handed bending force to the stalk. We used cryoEM to image yeast mitochondrial ATP synthase under strain during ATP-hydrolysis-driven rotary catalysis, revealing a large deformation of the peripheral stalk. The structures show how the peripheral stalk opposes the bending force and suggests that during ATP synthesis proton translocation causes accumulation of strain in the stalk, which relaxes by driving the relative rotation of the rotor through six sub-steps within F, leading to catalysis. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.5 KB 23.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.8 KB | Display | ![]() |
Images | ![]() | 82 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6.8 KB | ||
Others | ![]() ![]() ![]() | 32.3 MB 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tjuMC ![]() 7tjsC ![]() 7tjtC ![]() 7tjvC ![]() 7tjwC ![]() 7tjxC ![]() 7tjyC ![]() 7tjzC ![]() 7tk0C ![]() 7tk1C ![]() 7tk2C ![]() 7tk3C ![]() 7tk4C ![]() 7tk5C ![]() 7tk6C ![]() 7tk7C ![]() 7tk8C ![]() 7tk9C ![]() 7tkaC ![]() 7tkbC ![]() 7tkcC ![]() 7tkdC ![]() 7tkeC ![]() 7tkfC ![]() 7tkgC ![]() 7tkhC ![]() 7tkiC ![]() 7tkjC ![]() 7tkkC ![]() 7tklC ![]() 7tkmC ![]() 7tknC ![]() 7tkoC ![]() 7tkpC ![]() 7tkqC ![]() 7tkrC ![]() 7tksC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.3075 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Unsharpened map.
File | emd_25932_additional_1.map | ||||||||||||
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Annotation | Unsharpened map. | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_25932_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_25932_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Yeast ATP synthase F1 region State 1-3binding beta_tight open wit...
Entire | Name: Yeast ATP synthase F1 region State 1-3binding beta_tight open without exogenous ATP |
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Components |
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-Supramolecule #1: Yeast ATP synthase F1 region State 1-3binding beta_tight open wit...
Supramolecule | Name: Yeast ATP synthase F1 region State 1-3binding beta_tight open without exogenous ATP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 400 KDa |
-Macromolecule #1: ATP synthase subunit alpha
Macromolecule | Name: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 55.007402 KDa |
Sequence | String: ASTKAQPTEV SSILEERIKG VSDEANLNET GRVLAVGDGI ARVFGLNNIQ AEELVEFSSG VKGMALNLEP GQVGIVLFGS DRLVKEGEL VKRTGNIVDV PVGPGLLGRV VDALGNPIDG KGPIDAAGRS RAQVKAPGIL PRRSVHEPVQ TGLKAVDALV P IGRGQREL ...String: ASTKAQPTEV SSILEERIKG VSDEANLNET GRVLAVGDGI ARVFGLNNIQ AEELVEFSSG VKGMALNLEP GQVGIVLFGS DRLVKEGEL VKRTGNIVDV PVGPGLLGRV VDALGNPIDG KGPIDAAGRS RAQVKAPGIL PRRSVHEPVQ TGLKAVDALV P IGRGQREL IIGDRQTGKT AVALDTILNQ KRWNNGSDES KKLYCVYVAV GQKRSTVAQL VQTLEQHDAM KYSIIVAATA SE AAPLQYL APFTAASIGE WFRDNGKHAL IVYDDLSKQA VAYRQLSLLL RRPPGREAYP GDVFYLHSRL LERAAKLSEK EGS GSLTAL PVIETQGGDV SAYIPTNVIS ITDGQIFLEA ELFYKGIRPA INVGLSVSRV GSAAQVKALK QVAGSLKLFL AQYR EVAAF AQFGSDLDAS TKQTLVRGER LTQLLKQNQY SPLATEEQVP LIYAGVNGHL DGIELSRIGE FESSFLSYLK SNHNE LLTE IREKGELSKE LLASLKSATE SFVATF UniProtKB: ATP synthase subunit alpha, mitochondrial |
-Macromolecule #2: ATP synthase subunit beta
Macromolecule | Name: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 51.181082 KDa |
Sequence | String: ASAAQSTPIT GKVTAVIGAI VDVHFEQSEL PAILNALEIK TPQGKLVLEV AQHLGENTVR TIAMDGTEGL VRGEKVLDTG GPISVPVGR ETLGRIINVI GEPIDERGPI KSKLRKPIHA DPPSFAEQST SAEILETGIK VVDLLAPYAR GGKIGLFGGA G VGKTVFIQ ...String: ASAAQSTPIT GKVTAVIGAI VDVHFEQSEL PAILNALEIK TPQGKLVLEV AQHLGENTVR TIAMDGTEGL VRGEKVLDTG GPISVPVGR ETLGRIINVI GEPIDERGPI KSKLRKPIHA DPPSFAEQST SAEILETGIK VVDLLAPYAR GGKIGLFGGA G VGKTVFIQ ELINNIAKAH GGFSVFTGVG ERTREGNDLY REMKETGVIN LEGESKVALV FGQMNEPPGA RARVALTGLT IA EYFRDEE GQDVLLFIDN IFRFTQAGSE VSALLGRIPS AVGYQPTLAT DMGLLQERIT TTKKGSVTSV QAVYVPADDL TDP APATTF AHLDATTVLS RGISELGIYP AVDPLDSKSR LLDAAVVGQE HYDVASKVQE TLQTYKSLQD IIAILGMDEL SEQD KLTVE RARKIQRFLS QPFAVAEVFT GIPGKLVRLK DTVASFKAVL EGKYDNIPEH AFYMVGGIED VVAKAEKLAA EAN UniProtKB: ATP synthase subunit beta, mitochondrial |
-Macromolecule #3: ATP synthase subunit gamma
Macromolecule | Name: ATP synthase subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 30.65716 KDa |
Sequence | String: ATLKEVEMRL KSIKNIEKIT KTMKIVASTR LSKAEKAKIS AKKMDEAEQL FYKNAETKNL DVEATETGAP KELIVAITSD KGLCGSIHS QLAKAVRRHL NDQPNADIVT IGDKIKMQLL RTHPNNIKLS INGIGKDAPT FQESALIADK LLSVMKAGTY P KISIFYND ...String: ATLKEVEMRL KSIKNIEKIT KTMKIVASTR LSKAEKAKIS AKKMDEAEQL FYKNAETKNL DVEATETGAP KELIVAITSD KGLCGSIHS QLAKAVRRHL NDQPNADIVT IGDKIKMQLL RTHPNNIKLS INGIGKDAPT FQESALIADK LLSVMKAGTY P KISIFYND PVSSLSFEPS EKPIFNAKTI EQSPSFGKFE IDTDANVPRD LFEYTLANQM LTAMAQGYAA EISARRNAMD NA SKNAGDM INRYSILYNR TRQAVITNEL VDIITGASSL G UniProtKB: ATP synthase subunit gamma, mitochondrial |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ![]() ChemComp-PO4: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 15 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Homemade / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 35 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 8817 / Average exposure time: 10.1 sec. / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 133843 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |