[English] 日本語
Yorodumi- EMDB-9201: T20S proteasome using Topaz at threshold t-3 with published picks... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9201 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | T20S proteasome using Topaz at threshold t-3 with published picks subtracted from Topaz (EMPIAR-10025 reprocessing) | |||||||||
Map data | Cryosparc v0 auto-sharpened map | |||||||||
Sample |
| |||||||||
Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Bepler T / Morin A / Brasch J / Shapiro L / Noble AJ / Berger 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9201.map.gz | 229.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-9201-v30.xml emd-9201.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
Images | emd_9201.png | 171.9 KB | ||
Masks | emd_9201_msk_1.map | 244.1 MB | Mask map | |
Others | emd_9201_additional.map.gz emd_9201_half_map_1.map.gz emd_9201_half_map_2.map.gz | 120 MB 226.8 MB 226.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9201 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9201 | HTTPS FTP |
-Validation report
Summary document | emd_9201_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_9201_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_9201_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9201 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9201 | HTTPS FTP |
-Related structure data
Related structure data | 9194C 9202C 9206C 9207C 9208C 9209C 9210C 9211C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_9201.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryosparc v0 auto-sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.6575 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_9201_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Cryosparc v0 unsharpened map
File | emd_9201_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryosparc v0 unsharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Cryosparc v0 half-map
File | emd_9201_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryosparc v0 half-map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Cryosparc v0 half-map
File | emd_9201_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryosparc v0 half-map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : T20S proteasome
Entire | Name: T20S proteasome |
---|---|
Components |
|
-Supramolecule #1: T20S proteasome
Supramolecule | Name: T20S proteasome / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Recombinant expression | Organism: Thermoplasma acidophilum (acidophilic) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.21 mg/mL |
---|---|
Buffer | pH: 7.8 / Details: 20 mM Tris, 150 mM NaCl |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 Details: Blot for 2.5 seconds before plunging. Vitrification carried out at room temperature.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 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 |