+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33073 | |||||||||
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Title | one tomogram of the neuron cortical cell | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Rattus (rat) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Jiang W / Guo Q | |||||||||
Funding support | 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: A transformation clustering algorithm and its application in polyribosomes structural profiling. Authors: Wenhong Jiang / Jonathan Wagner / Wenjing Du / Juergen Plitzko / Wolfgang Baumeister / Florian Beck / Qiang Guo / Abstract: Improvements in cryo-electron tomography sample preparation, electron-microscopy instrumentations, and image processing algorithms have advanced the structural analysis of macromolecules in situ. ...Improvements in cryo-electron tomography sample preparation, electron-microscopy instrumentations, and image processing algorithms have advanced the structural analysis of macromolecules in situ. Beyond such analyses of individual macromolecules, the study of their interactions with functionally related neighbors in crowded cellular habitats, i.e. 'molecular sociology', is of fundamental importance in biology. Here we present a NEighboring Molecule TOpology Clustering (NEMO-TOC) algorithm. We optimized this algorithm for the detection and profiling of polyribosomes, which play both constitutive and regulatory roles in gene expression. Our results suggest a model where polysomes are formed by connecting multiple nonstochastic blocks, in which translation is likely synchronized. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33073.map.gz | 1.1 GB | EMDB map data format | |
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Header (meta data) | emd-33073-v30.xml emd-33073.xml | 7.8 KB 7.8 KB | Display Display | EMDB header |
Images | emd_33073.png | 200.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33073 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33073 | HTTPS FTP |
-Validation report
Summary document | emd_33073_validation.pdf.gz | 516.2 KB | Display | EMDB validaton report |
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Full document | emd_33073_full_validation.pdf.gz | 515.7 KB | Display | |
Data in XML | emd_33073_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | emd_33073_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33073 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33073 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33073.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 13.68 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : one tomogram of neuron cortical cell
Entire | Name: one tomogram of neuron cortical cell |
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Components |
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-Supramolecule #1: one tomogram of neuron cortical cell
Supramolecule | Name: one tomogram of neuron cortical cell / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Rattus (rat) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.5 nA / Focused ion beam - Duration: 1800 sec. / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 150 nm Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Thermo FisherAquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 61 |
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