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Yorodumi- EMDB-1542: Three-dimensional structure of Pyrococcus furiosus A1Ao ATP synthase -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1542 | |||||||||
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Title | Three-dimensional structure of Pyrococcus furiosus A1Ao ATP synthase | |||||||||
Map data | volume of Pyrococcus furiosus A-type ATP synthase | |||||||||
Sample |
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Keywords | ATP synthase / A1Ao ATP synthase | |||||||||
Biological species | Pyrococcus furiosus (archaea) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.0 Å | |||||||||
Authors | Vonck J / Pisa KY / Morgner N / Brutschy B / Mueller V | |||||||||
Citation | Journal: J Biol Chem / Year: 2009 Title: Three-dimensional structure of A1A0 ATP synthase from the hyperthermophilic archaeon Pyrococcus furiosus by electron microscopy. Authors: Janet Vonck / Kim Y Pisa / Nina Morgner / Bernhard Brutschy / Volker Müller / Abstract: The archaeal ATP synthase is a multisubunit complex that consists of a catalytic A(1) part and a transmembrane, ion translocation domain A(0). The A(1)A(0) complex from the hyperthermophile ...The archaeal ATP synthase is a multisubunit complex that consists of a catalytic A(1) part and a transmembrane, ion translocation domain A(0). The A(1)A(0) complex from the hyperthermophile Pyrococcus furiosus was isolated. Mass analysis of the complex by laser-induced liquid bead ion desorption (LILBID) indicated a size of 730 +/- 10 kDa. A three-dimensional map was generated by electron microscopy from negatively stained images. The map at a resolution of 2.3 nm shows the A(1) and A(0) domain, connected by a central stalk and two peripheral stalks, one of which is connected to A(0), and both connected to A(1) via prominent knobs. X-ray structures of subunits from related proteins were fitted to the map. On the basis of the fitting and the LILBID analysis, a structural model is presented with the stoichiometry A(3)B(3)CDE(2)FH(2)ac(10). | |||||||||
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_1542.map.gz | 516.8 KB | EMDB map data format | |
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Header (meta data) | emd-1542-v30.xml emd-1542.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | 1542.gif | 19.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1542 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1542 | HTTPS FTP |
-Validation report
Summary document | emd_1542_validation.pdf.gz | 198.5 KB | Display | EMDB validaton report |
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Full document | emd_1542_full_validation.pdf.gz | 197.6 KB | Display | |
Data in XML | emd_1542_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1542 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1542 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1542.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | volume of Pyrococcus furiosus A-type ATP synthase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.77 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : A1Ao ATP synthase from Pyrococcus furiosus
Entire | Name: A1Ao ATP synthase from Pyrococcus furiosus |
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Components |
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-Supramolecule #1000: A1Ao ATP synthase from Pyrococcus furiosus
Supramolecule | Name: A1Ao ATP synthase from Pyrococcus furiosus / type: sample / ID: 1000 / Oligomeric state: nine different subunits / Number unique components: 9 |
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Molecular weight | Experimental: 738 KDa / Theoretical: 738 KDa / Method: LILBID mass spectroscopy |
-Macromolecule #1: A1Ao ATP synthase
Macromolecule | Name: A1Ao ATP synthase / type: protein_or_peptide / ID: 1 / Name.synonym: ATP synthase / Oligomeric state: heteromultimer / Recombinant expression: No |
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Source (natural) | Organism: Pyrococcus furiosus (archaea) / Cell: archaeon / Location in cell: plasma membrane |
Molecular weight | Experimental: 738 KDa / Theoretical: 738 KDa |
-Macromolecule #2: A1Ao ATP synthase
Macromolecule | Name: A1Ao ATP synthase / type: protein_or_peptide / ID: 2 / Name.synonym: ATP synthase / Recombinant expression: No |
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Source (natural) | Organism: Pyrococcus furiosus (archaea) |
Molecular weight | Experimental: 738 KDa / Theoretical: 738 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 Details: 50 mM this/HCl, 5 mM MgCl2, 10% glycerol, 50 mM KCl, 0.1% Triton-X100, 0.1 mM PMSF |
Staining | Type: NEGATIVE Details: a drop of 1% (w/v) uranyl acetate was added to a carbon-coated grid with absorbed protein and blotted after 30 s. |
Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI/PHILIPS CM120T |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 160,000 times magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 51 / Average electron dose: 20 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 44000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 0.4 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder: eucentric / Specimen holder model: OTHER |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 12912 |
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Final two d classification | Number classes: 392 |