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Yorodumi- EMDB-10858: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -
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-Basic information
Entry | Database: EMDB / ID: EMD-10858 | ||||||||||||
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Title | Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - central stalk/cring | ||||||||||||
Map data | Local-resolution filtered full map of T. thermophila ATP synthase central stalk/c-ring | ||||||||||||
Sample |
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Keywords | mitochondria / ATP synthase / central stalk / c-ring / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information : / : / proton-transporting ATP synthase complex, coupling factor F(o) / proton transmembrane transporter activity / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / mitochondrion Similarity search - Function | ||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Kock Flygaard R / Muhleip A | ||||||||||||
Funding support | Sweden, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization. Authors: Rasmus Kock Flygaard / Alexander Mühleip / Victor Tobiasson / Alexey Amunts / Abstract: Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we ...Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature. | ||||||||||||
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_10858.map.gz | 472.2 MB | EMDB map data format | |
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Header (meta data) | emd-10858-v30.xml emd-10858.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10858_fsc.xml | 21.1 KB | Display | FSC data file |
Images | emd_10858.png | 37.3 KB | ||
Masks | emd_10858_msk_1.map | 824 MB | Mask map | |
Filedesc metadata | emd-10858.cif.gz | 5.7 KB | ||
Others | emd_10858_half_map_1.map.gz emd_10858_half_map_2.map.gz | 671.4 MB 672.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10858 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10858 | HTTPS FTP |
-Validation report
Summary document | emd_10858_validation.pdf.gz | 359.1 KB | Display | EMDB validaton report |
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Full document | emd_10858_full_validation.pdf.gz | 358.3 KB | Display | |
Data in XML | emd_10858_validation.xml.gz | 24.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10858 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10858 | HTTPS FTP |
-Related structure data
Related structure data | 6ynwMC 6ynvC 6ynxC 6ynyC 6ynzC 6yo0C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10858.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Local-resolution filtered full map of T. thermophila ATP synthase central stalk/c-ring | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 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_10858_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_10858_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_10858_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mitochondrial ATP synthase, central stalk/c-ring
Entire | Name: Mitochondrial ATP synthase, central stalk/c-ring |
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Components |
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-Supramolecule #1: Mitochondrial ATP synthase, central stalk/c-ring
Supramolecule | Name: Mitochondrial ATP synthase, central stalk/c-ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
-Macromolecule #1: subunit c
Macromolecule | Name: subunit c / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: ec: 3.6.1.34 |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 8.083702 KDa |
Sequence | String: MLLVKAVKVL VMGGCMLPIA FGALGTGVLF AGFNVALSRN PEETESLFNN TLMGFALIET FIFMSIGLGF FVLFAA UniProtKB: ATP synthase F0 subunit 9 |
-Macromolecule #2: subunit gamma
Macromolecule | Name: subunit gamma / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 32.915152 KDa |
Sequence | String: MFGLASKGFI NTSLVMVPQM NFGANLKQLK IRMKAIGSIK KITKAMKMVA ASKMKAETSR LENGRNFAVG SVQKMLENES YVQKKKSTT APKSTLLVPI TSDKGLCGSV NSSIVREVKR LALNNRSAFG LLPVGEKGSS GLSRPFPDLL KSSIVNIQNV N FPTAAAIA ...String: MFGLASKGFI NTSLVMVPQM NFGANLKQLK IRMKAIGSIK KITKAMKMVA ASKMKAETSR LENGRNFAVG SVQKMLENES YVQKKKSTT APKSTLLVPI TSDKGLCGSV NSSIVREVKR LALNNRSAFG LLPVGEKGSS GLSRPFPDLL KSSIVNIQNV N FPTAAAIA HQVSTQGAGY DQVTLIYNHF KNAISYVVKH QELLPRAQFL NLFKYVTRHE AVEPELEYSK NYFFELYMAS SV YNALLNS SASEQASRMN AMENASKNAG EILSKLTLDY NKARQAKITM ELIEIISGAS IV UniProtKB: ATP synthase subunit gamma |
-Macromolecule #3: subunit delta
Macromolecule | Name: subunit delta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 17.892537 KDa |
Sequence | String: MFTRFVTQPT LLTQTQRALF SALTKKQKME VTLRTPYKEY LANFDGFSRI TAKTNEASLV IQNKTPASLY VLPPGPLKIR FTSEVKNVS GDFLHTGGWV IVHADNTCEI NVMDLFDRKE VRADQFEKGN IQDLDTLAGK YAAKSRKSTV RLFTKATTQ UniProtKB: Uncharacterized protein |
-Macromolecule #4: subunit epsilon
Macromolecule | Name: subunit epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 7.986336 KDa |
Sequence | String: MCIEFAFKKA GIPIVRNFLH STEGVIYGLP QRVQRNLAIN YTVKQYKEGK AVSAKTIKTL QEAFPSKGDT K UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.75 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-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 / Average electron dose: 30.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 165000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |