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Yorodumi- EMDB-0399: Electron microscopy snapshots of single particles from single cells -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0399 | |||||||||
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Title | Electron microscopy snapshots of single particles from single cells | |||||||||
Map data | Reconstruction of 60S ribosome | |||||||||
Sample |
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Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 34.0 Å | |||||||||
Authors | Yi X / Verbeke EJ / Yiran C / Dickinson DJ / Taylor DW | |||||||||
Citation | Journal: J Biol Chem / Year: 2019 Title: Electron microscopy snapshots of single particles from single cells. Authors: Xiunan Yi / Eric J Verbeke / Yiran Chang / Daniel J Dickinson / David W Taylor / Abstract: Cryo-electron microscopy (cryo-EM) has become an indispensable tool for structural studies of biological macromolecules. Two additional predominant methods are available for studying the ...Cryo-electron microscopy (cryo-EM) has become an indispensable tool for structural studies of biological macromolecules. Two additional predominant methods are available for studying the architectures of multiprotein complexes: 1) single-particle analysis of purified samples and 2) tomography of whole cells or cell sections. The former can produce high-resolution structures but is limited to highly purified samples, whereas the latter can capture proteins in their native state but has a low signal-to-noise ratio and yields lower-resolution structures. Here, we present a simple, adaptable method combining microfluidic single-cell extraction with single-particle analysis by EM to characterize protein complexes from individual embryos. Using this approach, we uncover 3D structures of ribosomes directly from single embryo extracts. Moreover, we investigated structural dynamics during development by counting the number of ribosomes per polysome in early and late embryos. This approach has significant potential applications for counting protein complexes and studying protein architectures from single cells in developmental, evolutionary, and disease contexts. | |||||||||
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_0399.map.gz | 1.4 MB | EMDB map data format | |
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Header (meta data) | emd-0399-v30.xml emd-0399.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | emd_0399.png | 98.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0399 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0399 | 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_0399.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of 60S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.6 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 : 60S ribosome from single cells
Entire | Name: 60S ribosome from single cells |
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Components |
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-Supramolecule #1: 60S ribosome from single cells
Supramolecule | Name: 60S ribosome from single cells / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Molecular weight | Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.4 |
Staining | Type: NEGATIVE / Material: Uranyl Acetate |
Grid | Details: unspecified |
-Electron microscopy
Microscope | JEOL 2010F |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN MULTISCAN / Average electron dose: 30.0 e/Å2 |
-Image processing
Particle selection | Number selected: 30000 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 3400 |