+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6219 | |||||||||
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Title | T. acidophilum 20S proteasome | |||||||||
Map data | Reconstruction of T. acidophilum 20S proteasome, using K2 summit camera at a low magnification | |||||||||
Sample |
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Keywords | T. acidophilum 20S proteasome | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Li X / Cheng Y | |||||||||
Citation | Journal: Nat Methods / Year: 2015 Title: De novo protein structure determination from near-atomic-resolution cryo-EM maps. Authors: Ray Yu-Ruei Wang / Mikhail Kudryashev / Xueming Li / Edward H Egelman / Marek Basler / Yifan Cheng / David Baker / Frank DiMaio / Abstract: We present a de novo model-building approach that combines predicted backbone conformations with side-chain fit to density to accurately assign sequence into density maps. This method yielded ...We present a de novo model-building approach that combines predicted backbone conformations with side-chain fit to density to accurately assign sequence into density maps. This method yielded accurate models for six of nine experimental maps at 3.3- to 4.8-Å resolution and produced a nearly complete model for an unsolved map containing a 660-residue heterodimeric protein. This method should enable rapid and reliable protein structure determination from near-atomic-resolution cryo-electron microscopy (cryo-EM) maps. | |||||||||
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_6219.map.gz | 115.9 MB | EMDB map data format | |
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Header (meta data) | emd-6219-v30.xml emd-6219.xml | 8.1 KB 8.1 KB | Display Display | EMDB header |
Images | 400_6219.gif 80_6219.gif | 56 KB 4.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6219 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6219 | HTTPS FTP |
-Validation report
Summary document | emd_6219_validation.pdf.gz | 78 KB | Display | EMDB validaton report |
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Full document | emd_6219_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_6219_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6219 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6219 | 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_6219.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of T. acidophilum 20S proteasome, using K2 summit camera at a low magnification | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.98 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 : T. acidophilum 20S proteasome
Entire | Name: T. acidophilum 20S proteasome |
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Components |
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-Supramolecule #1000: T. acidophilum 20S proteasome
Supramolecule | Name: T. acidophilum 20S proteasome / type: sample / ID: 1000 / Oligomeric state: 28-mer / Number unique components: 1 |
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Molecular weight | Experimental: 700 KDa / Theoretical: 700 KDa |
-Macromolecule #1: 20S proteasome
Macromolecule | Name: 20S proteasome / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: 24-mer / Recombinant expression: Yes |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Experimental: 700 KDa / Theoretical: 700 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Grid | Details: Holey carbon on top of 400 mesh grid |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Details | Images were recorded in dose-fractionated format using K2 Summit operated in counting and super-resolution mode. Motion correction was performed for each image. |
Date | Jan 1, 2012 |
Image recording | Category: CCD / Film or detector model: OTHER / Number real images: 157 / Average electron dose: 30 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.9 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 20000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: OTHER / Software - Name: FREALIGN / Number images used: 79801 |