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Yorodumi- EMDB-3456: Thermoplasma acidophilum 20S proteasome map reconstructed with Mo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3456 | |||||||||
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Title | Thermoplasma acidophilum 20S proteasome map reconstructed with MotionCor2 and Relion 2.0 from defocused Volta phase plate cryo-EM data | |||||||||
Map data | Thermoplasma acidophilum 20S proteasome map reconstructed with MotionCor2 and Relion 2.0 from defocused Volta phase plate cryo-EM data. | |||||||||
Sample |
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Biological species | Thermoplasma acidophilum (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Danev R / Tegunov D / Baumeister W | |||||||||
Citation | Journal: Elife / Year: 2017 Title: Using the Volta phase plate with defocus for cryo-EM single particle analysis. Authors: Radostin Danev / Dimitry Tegunov / Wolfgang Baumeister / Abstract: Previously, we reported an in-focus data acquisition method for cryo-EM single-particle analysis with the Volta phase plate (Danev and Baumeister, 2016). Here, we extend the technique to include a ...Previously, we reported an in-focus data acquisition method for cryo-EM single-particle analysis with the Volta phase plate (Danev and Baumeister, 2016). Here, we extend the technique to include a small amount of defocus which enables contrast transfer function measurement and correction. This hybrid approach simplifies the experiment and increases the data acquisition speed. It also removes the resolution limit inherent to the in-focus method thus allowing 3D reconstructions with resolutions better than 3 Å. | |||||||||
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_3456.map.gz | 166.5 MB | EMDB map data format | |
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Header (meta data) | emd-3456-v30.xml emd-3456.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_3456.png | 241.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3456 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3456 | HTTPS FTP |
-Validation report
Summary document | emd_3456_validation.pdf.gz | 336.1 KB | Display | EMDB validaton report |
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Full document | emd_3456_full_validation.pdf.gz | 335.3 KB | Display | |
Data in XML | emd_3456_validation.xml.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3456 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3456 | HTTPS FTP |
-Related structure data
Related structure data | 3455C 3457C C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10078 (Title: Volta phase plate with defocus cryo-EM dataset of Thermoplasma acidophilum 20S proteasome Data size: 92.5 Data #1: Unaligned multi-frame micrographs of 20S proteasome acquired with a Volta phase plate and defocus [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3456.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Thermoplasma acidophilum 20S proteasome map reconstructed with MotionCor2 and Relion 2.0 from defocused Volta phase plate cryo-EM data. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.53 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 : Thermoplasma acidophilum 20S proteasome
Entire | Name: Thermoplasma acidophilum 20S proteasome |
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Components |
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-Supramolecule #1: Thermoplasma acidophilum 20S proteasome
Supramolecule | Name: Thermoplasma acidophilum 20S proteasome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Thermoplasma acidophilum (acidophilic) |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Recombinant plasmid: pT7-7 |
Molecular weight | Theoretical: 700 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.6 / Details: 25 mM Tris-HCL |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.1 kPa |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK III Details: 3 ul of 0.5 mg/ml protein solution was applied on a grid in the Vitrobot chamber set to 95% RH at 20 degC then blotted for 5 s and plunged. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 3-24 / Number grids imaged: 1 / Number real images: 468 / Average exposure time: 12.0 sec. / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 0.7 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.62 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 85 |
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