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Yorodumi- EMDB-13184: Subtomogram average of Axonemal Doublet Microtubule from Tetrahym... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13184 | |||||||||
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Title | Subtomogram average of Axonemal Doublet Microtubule from Tetrahymena thermophila | |||||||||
Map data | Subtomogram average of Axonemal Doublet Microtubule from Tetrahymena thermophila | |||||||||
Sample |
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Biological species | Tetrahymena thermophila CU428 (eukaryote) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 12.3 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_13184.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-13184-v30.xml emd-13184.xml | 7.2 KB 7.2 KB | Display Display | EMDB header |
Images | emd_13184.png | 55.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13184 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13184 | HTTPS FTP |
-Validation report
Summary document | emd_13184_validation.pdf.gz | 235.7 KB | Display | EMDB validaton report |
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Full document | emd_13184_full_validation.pdf.gz | 234.8 KB | Display | |
Data in XML | emd_13184_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | emd_13184_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13184 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13184 | 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_13184.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram average of Axonemal Doublet Microtubule from Tetrahymena thermophila | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.3 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 : Axonemal Doublet Microtubule from Tetrahymena thermophila
Entire | Name: Axonemal Doublet Microtubule from Tetrahymena thermophila |
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Components |
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-Supramolecule #1: Axonemal Doublet Microtubule from Tetrahymena thermophila
Supramolecule | Name: Axonemal Doublet Microtubule from Tetrahymena thermophila type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Tetrahymena thermophila CU428 (eukaryote) |
-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 TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 9540 |
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Extraction | Number tomograms: 24 / Number images used: 9540 |
Final angle assignment | Type: OTHER |