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- EMDB-8446: Structure of bL17-depleted large ribosomal subunit assembly inter... -
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Open data
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Basic information
Entry | Database: EMDB / ID: 8446 |
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Title | Structure of bL17-depleted large ribosomal subunit assembly intermediate - Class D1 |
![]() | Class D1 bL17-Depleted 50S Ribosomal Biogenesis Intermediate |
![]() | bL17-depleted large ribosomal subunit assembly intermediate - Class D1: |
Source | ![]() ![]() ![]() |
Method | ![]() ![]() |
![]() | Tan Y / Davis JH / Lyumkis D |
![]() | Journal: Cell / Year: 2016 Title: Modular Assembly of the Bacterial Large Ribosomal Subunit. ![]() Abstract: The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as ...The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to ∼4-5 Å resolution and could be placed in an assembly pathway. We find that ribosome biogenesis is a parallel process, that blocks of structured rRNA and proteins assemble cooperatively, and that the entire process is dynamic and can be "re-routed" through different pathways as needed. This work reveals the complex landscape of ribosome assembly in vivo and provides the requisite tools to characterize additional assembly pathways for ribosomes and other macromolecular machines. |
Date | Deposition: Oct 25, 2016 / Header (metadata) release: Nov 16, 2016 / Map release: Dec 14, 2016 / Last update: Feb 14, 2018 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
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Header (meta data in XML format) | ![]() ![]() ![]() |
FSC (resolution estimation) | ![]() |
Images | ![]() |
Masks (Map data of sub-region, etc) | ![]() |
Others | ![]() ![]() ![]() |
FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8446 |
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Links
EMDB pages | ![]() ![]() |
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EM raw data | ![]() Data size: 50.3 Data #1: Particle stack of L17-depleted 50S Ribosomal Assembly Intermediates [picked particles - multiframe - unprocessed]) |
-Related structure data
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire bL17-depleted large ribosomal subunit assembly intermediate - Class D1
Entire | Name: bL17-depleted large ribosomal subunit assembly intermediate - Class D1 Details: E. coli large ribosome subunit purified from bL17-depleted cells. Number of components: 1 |
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-Component #1: protein, bL17-depleted large ribosomal subunit assembly intermedi...
Protein | Name: bL17-depleted large ribosomal subunit assembly intermediate - Class D1 Details: E. coli large ribosome subunit purified from bL17-depleted cells. Recombinant expression: No |
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Source | Species: ![]() ![]() ![]() |
-Experimental details
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Sample preparation
Specimen | Specimen state: particle / Method: ![]() |
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Sample solution | Buffer solution: Most of the sucrose was removed by spin concentration pH: 7.5 |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 80 % / Details: 3 microliter of the sample was added.. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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![]() | Microscope: FEI TITAN KRIOS Details: In order to account for highly preferred orientation of the specimen, data was acquired using tilts ranging from 10-60 degrees, in addition to untilted images at 0 degrees. The CTF was estimated on a per-particle basis to account for the gradient of CTF values across individual micrographs |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 22500.0 X (nominal), 38167.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: FEI TITAN KRIOS AUTOGRID HOLDER |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
-Image acquisition
Image acquisition | Number of digital images: 2479 / Sampling size: 5 microns |
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Raw data | ![]() Data size: 50.3 Data #1: Particle stack of L17-depleted 50S Ribosomal Assembly Intermediates [picked particles - multiframe - unprocessed]) |