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Yorodumi- EMDB-10470: Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase,... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10470 | |||||||||
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Title | Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, rotor, rotational state 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | mitochondria / ATP synthase / MEMBRANE PROTEIN | |||||||||
Biological species | Euglena gracilis (euglena) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Muhleip A / Amunts A | |||||||||
Citation | Journal: Elife / Year: 2019 Title: Structure of a mitochondrial ATP synthase with bound native cardiolipin. Authors: Alexander Mühleip / Sarah E McComas / Alexey Amunts / Abstract: The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum ...The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 Å resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit . The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF) binds in a mode that is different from human, but conserved in Trypanosomatids. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10470.map.gz | 288.1 MB | EMDB map data format | |
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Header (meta data) | emd-10470-v30.xml emd-10470.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_10470.png | 33.8 KB | ||
Masks | emd_10470_msk_1.map | 325 MB | Mask map | |
Filedesc metadata | emd-10470.cif.gz | 5.7 KB | ||
Others | emd_10470_half_map_1.map.gz emd_10470_half_map_2.map.gz | 258.9 MB 260.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10470 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10470 | HTTPS FTP |
-Validation report
Summary document | emd_10470_validation.pdf.gz | 352.3 KB | Display | EMDB validaton report |
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Full document | emd_10470_full_validation.pdf.gz | 351.4 KB | Display | |
Data in XML | emd_10470_validation.xml.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10470 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10470 | HTTPS FTP |
-Related structure data
Related structure data | 6tdxMC 6tduC 6tdvC 6tdwC 6tdyC 6tdzC 6te0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10470.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10470_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10470_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10470_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Euglena gracilis mitochondrial ATP synthase dimer
Entire | Name: Euglena gracilis mitochondrial ATP synthase dimer |
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Components |
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-Supramolecule #1: Euglena gracilis mitochondrial ATP synthase dimer
Supramolecule | Name: Euglena gracilis mitochondrial ATP synthase dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 2 MDa |
-Macromolecule #1: ATP synthase F1 subunit gamma
Macromolecule | Name: ATP synthase F1 subunit gamma / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 35.110375 KDa |
Sequence | String: MPGGGTIRFW REKLEGYKKY HQIVKTIKMV TLAKYRQTVV RTRVRDQTLR YTRKALDAKT QDDQEVIEKS ECLLYVPITT NRGSCGALN TNMVRYLQEV ENPKMTIISV GKKALDAMTK VFQDTYRRTI LNDMKQAMSF QFAAYVLEHM NTVPWDRAQI V YNRYHGAA ...String: MPGGGTIRFW REKLEGYKKY HQIVKTIKMV TLAKYRQTVV RTRVRDQTLR YTRKALDAKT QDDQEVIEKS ECLLYVPITT NRGSCGALN TNMVRYLQEV ENPKMTIISV GKKALDAMTK VFQDTYRRTI LNDMKQAMSF QFAAYVLEHM NTVPWDRAQI V YNRYHGAA SQKLAIFNLP KFEDWKQKLE EDSAGDGKIE EDGLLQSLPM KTALGELEET AVEDFYNFHS CLAVLNAVSE NE LSEYAAR IVAVENQLGN ITGLMQLADY TYNKTRKELI TAELLEIIGT MTAMHAGKKV GLKKTEFWK |
-Macromolecule #2: F-type H+-transporting ATPase subunit delta
Macromolecule | Name: F-type H+-transporting ATPase subunit delta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 19.559953 KDa |
Sequence | String: MRASRTLLLS VSRFMRQDPR KFFPDNGFRF FDGPEDSFGD GNIPAQIILT LTRQDEFILK QEPVAAITIR TNEGEMGVLA GHEYTVQQL APGILEVEYE GGKKDQYVIS GGFAHVNDTG VVDINTVEAV PLEEIDHEKL AKALEEARAK SQSPDEAVRI Q GEIALEIF EPLEAALH |
-Macromolecule #3: ATP synthase F1 subunit epsilon
Macromolecule | Name: ATP synthase F1 subunit epsilon / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 8.751981 KDa |
Sequence | String: MSWRDAGISY LRYLSIVTRC IHEVQKEGPL LTKNVRFSTI GWKSLYLDHG ATKEYTAIPA ELEKIPENQV AQQHHA |
-Macromolecule #4: ATP synthase subunit c
Macromolecule | Name: ATP synthase subunit c / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 10.820831 KDa |
Sequence | String: MQRGSSITKV VRRAALARST RNAAIAYEVT VNGANLIGAG MAASGVGVPA IGVAMCFSSY MLAAARQPNM SAKLLPYCIL GFALSEALA LFTLLIALLE LFVFS |
-Macromolecule #5: ATPEG1
Macromolecule | Name: ATPEG1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Euglena gracilis (euglena) |
Molecular weight | Theoretical: 19.708709 KDa |
Sequence | String: MSLAKVWTYA SWIPRGIPKA MANELSSAAA ALAHPEAIAR VAQLESQGKN PYRVARAEFW QMYLACWPYR FRNTVVEWET CKAKVLKGS VDLQDIVDLL YLLAWAYLFW ILGEIYGRGS LYGYRFDGEI HRQEAQNVIL YKEKEAQEMA VVMEKLEKEI Q EWLKTMEQ E |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds blot. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 9045 / Average exposure time: 10.0 sec. / Average electron dose: 36.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |