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Yorodumi- EMDB-13183: Subtomogram average of T20S proteasome from Thermoplasma acidophilum -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13183 | |||||||||
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Title | Subtomogram average of T20S proteasome from Thermoplasma acidophilum | |||||||||
Map data | Subtomogram average of T20S proteasome from Thermoplasma acidophilum | |||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Fernandez JJ / Li S | |||||||||
Citation | Journal: J Struct Biol / Year: 2021 Title: TomoAlign: A novel approach to correcting sample motion and 3D CTF in CryoET. Authors: Jose-Jesus Fernandez / Sam Li / Abstract: TomoAlign is a software package that integrates tools to mitigate two important resolution limiting factors in cryoET, namely the beam-induced sample motion and the contrast transfer function (CTF) ...TomoAlign is a software package that integrates tools to mitigate two important resolution limiting factors in cryoET, namely the beam-induced sample motion and the contrast transfer function (CTF) of the microscope. The package is especially focused on cryoET of thick specimens where fiducial markers are required for accurate tilt-series alignment and sample motion estimation. TomoAlign models the beam-induced sample motion undergone during the tilt-series acquisition. The motion models are used to produce motion-corrected subtilt-series centered on the particles of interest. In addition, the defocus of each particle at each tilt image is determined and can be corrected, resulting in motion-corrected and CTF-corrected subtilt-series from which the subtomograms can be computed. Alternatively, the CTF information can be passed on so that CTF correction can be carried out entirely within external packages like Relion. TomoAlign serves as a versatile tool that can streamline the cryoET workflow from initial alignment of tilt-series to final subtomogram averaging during in situ structure determination. | |||||||||
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_13183.map.gz | 6.3 MB | EMDB map data format | |
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Header (meta data) | emd-13183-v30.xml emd-13183.xml | 7.1 KB 7.1 KB | Display Display | EMDB header |
Images | emd_13183.png | 33 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13183 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13183 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13183.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram average of T20S proteasome from Thermoplasma acidophilum | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.56 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 : T20S proteasome
Entire | Name: T20S proteasome |
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Components |
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-Supramolecule #1: T20S proteasome
Supramolecule | Name: T20S proteasome / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 14 / Number images used: 3928 |
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Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 3928 |