+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8590 | |||||||||
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Title | Subtomogram average of ribosome from Trypanosoma brucei | |||||||||
Map data | Subtomogram average of ribosome from Trypanosoma brucei | |||||||||
Sample |
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Function / homology | Function and homology information organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / positive regulation of translational fidelity / mitochondrial large ribosomal subunit / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...organellar small ribosomal subunit / organellar large ribosomal subunit / ciliary transition zone / nuclear lumen / positive regulation of translational fidelity / mitochondrial large ribosomal subunit / phosphate ion binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosomal large subunit assembly / maturation of SSU-rRNA / small-subunit processome / regulation of cell growth / protein kinase C binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / regulation of cell population proliferation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / enzyme binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Trypanosoma brucei (eukaryote) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 38.5 Å | |||||||||
Authors | Chen M / Sun SY / Ludtke SJ / He CY / Schmid MF / Chiu W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Methods / Year: 2017 Title: Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Authors: Muyuan Chen / Wei Dai / Stella Y Sun / Darius Jonasch / Cynthia Y He / Michael F Schmid / Wah Chiu / Steven J Ludtke / Abstract: Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components ...Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components within the crowded cellular environment. We introduce a method that uses neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction. Subsequent subtomogram classification and averaging yield in situ structures of molecular components of interest. The method is available in the EMAN2.2 software package. | |||||||||
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_8590.map.gz | 84.9 KB | EMDB map data format | |
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Header (meta data) | emd-8590-v30.xml emd-8590.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | emd_8590.png | 24.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8590 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8590 | HTTPS FTP |
-Validation report
Summary document | emd_8590_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_8590_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_8590_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8590 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8590 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8590.map.gz / Format: CCP4 / Size: 432.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram average of ribosome from Trypanosoma brucei | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10.6 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 : Ribosomes in cell
Entire | Name: Ribosomes in cell |
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Components |
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-Supramolecule #1: Ribosomes in cell
Supramolecule | Name: Ribosomes in cell / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Trypanosoma brucei (eukaryote) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL 2200FS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Detector mode: INTEGRATING / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 38.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.2) / Number subtomograms used: 511 |
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Extraction | Number tomograms: 1 / Number images used: 759 / Method: Automated tomogram segmentation / Software - Name: EMAN (ver. 2.2) / Software - details: Tomoseg tool |
Final angle assignment | Type: OTHER / Software - Name: EMAN (ver. 2.2) / Details: Single particle tomography tool in EMAN2 |