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- EMDB-2460: 30S Ribosome Subunit Assembly Intermediates, Intermediate Group 1a -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2460 | |||||||||
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Title | 30S Ribosome Subunit Assembly Intermediates, Intermediate Group 1a | |||||||||
![]() | Intermediate Group 1a | |||||||||
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![]() | Ribosome Assembly / 30S Ribosome Subunit / 30S Assembly / Time-resolved electron microscopy / Discovery Single-particle Profiling / 30S Ribosome Subunit Assembly Intermediate | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 66.12 Å | |||||||||
![]() | Mulder AM / Yoshioka C / Beck A / Bunner A / Milligan RA / Potter CS / Carragher B / Williamson JR | |||||||||
![]() | ![]() Title: Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit. Authors: Anke M Mulder / Craig Yoshioka / Andrea H Beck / Anne E Bunner / Ronald A Milligan / Clinton S Potter / Bridget Carragher / James R Williamson / ![]() Abstract: Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the ...Ribosomes are self-assembling macromolecular machines that translate DNA into proteins, and an understanding of ribosome biogenesis is central to cellular physiology. Previous studies on the Escherichia coli 30S subunit suggest that ribosome assembly occurs via multiple parallel pathways rather than through a single rate-limiting step, but little mechanistic information is known about this process. Discovery single-particle profiling (DSP), an application of time-resolved electron microscopy, was used to obtain more than 1 million snapshots of assembling 30S subunits, identify and visualize the structures of 14 assembly intermediates, and monitor the population flux of these intermediates over time. DSP results were integrated with mass spectrometry data to construct the first ribosome-assembly mechanism that incorporates binding dependencies, rate constants, and structural characterization of populated intermediates. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 7.5 KB 7.5 KB | Display Display | ![]() |
Images | ![]() | 114.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1783C ![]() 2453C ![]() 2454C ![]() 2455C ![]() 2456C ![]() 2457C ![]() 2458C ![]() 2461C ![]() 2465C ![]() 2466C ![]() 2467C ![]() 2468C ![]() 2469C ![]() 2470C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Intermediate Group 1a | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.55 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : 30S Reconstitution Reaction
Entire | Name: 30S Reconstitution Reaction |
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Components |
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-Supramolecule #1000: 30S Reconstitution Reaction
Supramolecule | Name: 30S Reconstitution Reaction / type: sample / ID: 1000 / Number unique components: 21 |
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Molecular weight | Theoretical: 789 KDa |
-Supramolecule #1: 30S Ribosome Subunit
Supramolecule | Name: 30S Ribosome Subunit / type: complex / ID: 1 / Name.synonym: 30S Subunit / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S, PSR16s |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 789 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 / Details: 25 mM Tris-HCl, 330 mM KCl, 20 mM MgCl2, 2 mM DTT |
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Staining | Type: NEGATIVE / Details: 2% UA |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Jan 7, 2009 |
Image recording | Number real images: 6635 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Single tilt / Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Ace2 |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 66.12 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Appion, Spider, Eman / Number images used: 1382 |