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Yorodumi- EMDB-21002: Cryo-EM structure of porcine ATP synthase reconstituted in small ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21002 | |||||||||
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Title | Cryo-EM structure of porcine ATP synthase reconstituted in small unilamellar vesicles_II | |||||||||
Map data | Cryo-EM structure of porcine ATP synthase | |||||||||
Sample |
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Biological species | Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 30.0 Å | |||||||||
Authors | Mnatsakanyan N / Llaguno MC / Yang Y / Yan Y / Weber J / Sigworth FJ / Jonas EA | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2019 Title: A mitochondrial megachannel resides in monomeric FF ATP synthase. Authors: Nelli Mnatsakanyan / Marc C Llaguno / Youshan Yang / Yangyang Yan / Joachim Weber / Fred J Sigworth / Elizabeth A Jonas / Abstract: Purified mitochondrial ATP synthase has been shown to form Ca-activated, large conductance channel activity similar to that of mitochondrial megachannel (MMC) or mitochondrial permeability transition ...Purified mitochondrial ATP synthase has been shown to form Ca-activated, large conductance channel activity similar to that of mitochondrial megachannel (MMC) or mitochondrial permeability transition pore (mPTP) but the oligomeric state required for channel formation is being debated. We reconstitute purified monomeric ATP synthase from porcine heart mitochondria into small unilamellar vesicles (SUVs) with the lipid composition of mitochondrial inner membrane and analyze its oligomeric state by electron cryomicroscopy. The cryo-EM density map reveals the presence of a single ATP synthase monomer with no density seen for a second molecule tilted at an 86 angle relative to the first. We show that this preparation of SUV-reconstituted ATP synthase monomers, when fused into giant unilamellar vesicles (GUVs), forms voltage-gated and Ca-activated channels with the key features of mPTP. Based on our findings we conclude that the ATP synthase monomer is sufficient, and dimer formation is not required, for mPTP activity. | |||||||||
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_21002.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-21002-v30.xml emd-21002.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21002_fsc.xml | 4.8 KB | Display | FSC data file |
Images | emd_21002.png | 66.3 KB | ||
Masks | emd_21002_msk_1.map | 8 MB | Mask map | |
Others | emd_21002_half_map_1.map.gz emd_21002_half_map_2.map.gz | 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21002 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21002 | HTTPS FTP |
-Validation report
Summary document | emd_21002_validation.pdf.gz | 79.3 KB | Display | EMDB validaton report |
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Full document | emd_21002_full_validation.pdf.gz | 78.4 KB | Display | |
Data in XML | emd_21002_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21002 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21002 | HTTPS FTP |
-Related structure data
Related structure data | 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_21002.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of porcine ATP synthase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.2 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_21002_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of porcine ATP synthase
File | emd_21002_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of porcine ATP synthase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of porcine ATP synthase
File | emd_21002_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of porcine ATP synthase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Purified ATP synthase reconstituted in liposomes
Entire | Name: Purified ATP synthase reconstituted in liposomes |
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Components |
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-Supramolecule #1: Purified ATP synthase reconstituted in liposomes
Supramolecule | Name: Purified ATP synthase reconstituted in liposomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Sus scrofa (pig) / Organ: Heart / Organelle: Mitochondria |
Molecular weight | Experimental: 750 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 / Details: 50 mM Tris-HCl, 150 mM NaCl, 2 mM MgSO4, 1 mM ATP |
Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | Purified ATP synthase reconstituted in liposomes |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 4.219 µm / Calibrated defocus min: 1.871 µm / Calibrated magnification: 47620 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |