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Yorodumi- EMDB-1676: CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase B... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1676 | |||||||||
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Title | CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of ADP | |||||||||
Map data | This is the volume of the complex of Magnesium Chelatase subunit BchI and BchD incubated with ADP. | |||||||||
Sample |
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Keywords | AAA+ atpase / metallation / tetrapyrroles / Mg chelatase | |||||||||
Function / homology | Function and homology information bacteriochlorophyll biosynthetic process / magnesium chelatase / magnesium chelatase activity / photosynthesis / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Rhodobacter capsulatus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 7.5 Å | |||||||||
Authors | Lundqvist J / Elmlund H / Peterson-Wulff R / Elmlund D / Emanuelsson C / Hebert H / Willows R / Hansson M / Lindahl M / Al-Karadaghi S | |||||||||
Citation | Journal: J Mol Biol / Year: 2008 Title: A new cryo-EM single-particle ab initio reconstruction method visualizes secondary structure elements in an ATP-fueled AAA+ motor. Authors: Hans Elmlund / Joakim Lundqvist / Salam Al-Karadaghi / Mats Hansson / Hans Hebert / Martin Lindahl / Abstract: The generation of ab initio three-dimensional (3D) models is a bottleneck in the studies of large macromolecular assemblies by single-particle cryo-electron microscopy. We describe here a novel ...The generation of ab initio three-dimensional (3D) models is a bottleneck in the studies of large macromolecular assemblies by single-particle cryo-electron microscopy. We describe here a novel method, in which established methods for two-dimensional image processing are combined with newly developed programs for joint rotational 3D alignment of a large number of class averages (RAD) and calculation of 3D volumes from aligned projections (VolRec). We demonstrate the power of the method by reconstructing an approximately 660-kDa ATP-fueled AAA+ motor to 7.5 A resolution, with secondary structure elements identified throughout the structure. We propose the method as a generally applicable automated strategy to obtain 3D reconstructions from unstained single particles imaged in vitreous ice. | |||||||||
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_1676.map.gz | 14 MB | EMDB map data format | |
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Header (meta data) | emd-1676-v30.xml emd-1676.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_1676.jpg | 47.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1676 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1676 | HTTPS FTP |
-Validation report
Summary document | emd_1676_validation.pdf.gz | 220.9 KB | Display | EMDB validaton report |
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Full document | emd_1676_full_validation.pdf.gz | 220.1 KB | Display | |
Data in XML | emd_1676_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1676 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1676 | HTTPS FTP |
-Related structure data
Related structure data | 2x31MC 1677C 1678C C: citing same article (ref.) M: atomic model generated by this map |
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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_1676.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the volume of the complex of Magnesium Chelatase subunit BchI and BchD incubated with ADP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.167 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 : Complex of Mg-chelatase subunits BchI and BchD in presence of ADP
Entire | Name: Complex of Mg-chelatase subunits BchI and BchD in presence of ADP |
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Components |
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-Supramolecule #1000: Complex of Mg-chelatase subunits BchI and BchD in presence of ADP
Supramolecule | Name: Complex of Mg-chelatase subunits BchI and BchD in presence of ADP type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 660 KDa / Theoretical: 660 KDa |
-Macromolecule #1: Biosynthetic enzyme
Macromolecule | Name: Biosynthetic enzyme / type: protein_or_peptide / ID: 1 / Name.synonym: Mg chelatase / Recombinant expression: Yes |
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Source (natural) | Organism: Rhodobacter capsulatus (bacteria) |
Molecular weight | Theoretical: 660 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 |
Staining | Type: NEGATIVE / Details: Vitrification |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 2010F |
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Image recording | Digitization - Scanner: ZEISS SCAI / Number real images: 18 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: JEOL |
-Image processing
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 29400 |
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Final two d classification | Number classes: 258 |