+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6287 | |||||||||
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Title | 2.8 Angstrom resolution reconstruction of the T20S proteasome | |||||||||
Map data | Reconstruction of the T20S proteasome at 2.8 Angstrom resolution | |||||||||
Sample |
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Keywords | Direct detectors / Image processing | |||||||||
Function / homology | Function and homology information proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / endopeptidase activity / ubiquitin-dependent protein catabolic process / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Campbell MG / Veesler D / Cheng A / Potter CS / Carragher B | |||||||||
Citation | Journal: Elife / Year: 2015 Title: 2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy. Authors: Melody G Campbell / David Veesler / Anchi Cheng / Clinton S Potter / Bridget Carragher / Abstract: Recent developments in detector hardware and image-processing software have revolutionized single particle cryo-electron microscopy (cryoEM) and led to a wave of near-atomic resolution (typically ...Recent developments in detector hardware and image-processing software have revolutionized single particle cryo-electron microscopy (cryoEM) and led to a wave of near-atomic resolution (typically ∼3.3 Å) reconstructions. Reaching resolutions higher than 3 Å is a prerequisite for structure-based drug design and for cryoEM to become widely interesting to pharmaceutical industries. We report here the structure of the 700 kDa Thermoplasma acidophilum 20S proteasome (T20S), determined at 2.8 Å resolution by single-particle cryoEM. The quality of the reconstruction enables identifying the rotameric conformation adopted by some amino-acid side chains (rotamers) and resolving ordered water molecules, in agreement with the expectations for crystal structures at similar resolutions. The results described in this manuscript demonstrate that single particle cryoEM is capable of competing with X-ray crystallography for determination of protein structures of suitable quality for rational drug design. | |||||||||
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_6287.map.gz | 17.4 MB | EMDB map data format | |
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Header (meta data) | emd-6287-v30.xml emd-6287.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_6287.jpg | 124.2 KB | ||
Others | emd_6287_additional_1.map.gz emd_6287_additional_2.map.gz emd_6287_half_map_1.map.gz emd_6287_half_map_2.map.gz | 80.7 MB 2 MB 80.9 MB 80.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6287 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6287 | HTTPS FTP |
-Validation report
Summary document | emd_6287_validation.pdf.gz | 77.9 KB | Display | EMDB validaton report |
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Full document | emd_6287_full_validation.pdf.gz | 77 KB | Display | |
Data in XML | emd_6287_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6287 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6287 | HTTPS FTP |
-Related structure data
Related structure data | 6bdfMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10025 (Title: T20S Proteasome at 2.8 Å Resolution / Data size: 2.0 TB / Data #1: Raw movies [micrographs - multiframe] Data #2: Frame-averaged micrographs [micrographs - single frame] Data #3: Aligned multi-frame micrographs [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6287.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the T20S proteasome at 2.8 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.982 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 6287 additional 1.map
File | emd_6287_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 6287 additional 2.map
File | emd_6287_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 6287 half map 1.map
File | emd_6287_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 6287 half map 2.map
File | emd_6287_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T20S Proteasome
Entire | Name: T20S Proteasome |
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Components |
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-Supramolecule #1000: T20S Proteasome
Supramolecule | Name: T20S Proteasome / type: sample / ID: 1000 / Oligomeric state: D7 / Number unique components: 1 |
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Molecular weight | Theoretical: 700 KDa |
-Macromolecule #1: 20S proteasome
Macromolecule | Name: 20S proteasome / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Oligomeric state: 28-mer / Recombinant expression: Yes |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Molecular weight | Theoretical: 700 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pREAR-A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.21 mg/mL |
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Buffer | pH: 7.8 / Details: 20 mM Tris, 150 mM NaCl |
Grid | Details: 1.2/1.3 C-Flat grid, plasma cleaned |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 95 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Vitrification carried out at room temperature. / Method: Blot for 2.5 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 22,500 times magnification. |
Date | Sep 5, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 192 / Average electron dose: 53 e/Å2 Details: Each movie was acquired over 7.6 seconds and comprises 38 frames. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37313 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 49954 |