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Yorodumi- EMDB-1927: Ribosome Assembly Factors Prevent Premature Translation Initiatio... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1927 | |||||||||
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Title | Ribosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates | |||||||||
Map data | surface render of wild type Pre-40s map | |||||||||
Sample |
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Keywords | pre-40S / Rio2-TAP / 40S intermediate | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 18.0 Å | |||||||||
Authors | Strunk BS / Loucks CR / Su M / Vashisth H / Cheng S / Schilling J / BrooksIII CL / Karbstein K / Skiniotis G | |||||||||
Citation | Journal: Science / Year: 2011 Title: Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates. Authors: Bethany S Strunk / Cherisse R Loucks / Min Su / Harish Vashisth / Shanshan Cheng / Justin Schilling / Charles L Brooks / Katrin Karbstein / Georgios Skiniotis / Abstract: Ribosome assembly in eukaryotes requires approximately 200 essential assembly factors (AFs) and occurs through ordered events that initiate in the nucleolus and culminate in the cytoplasm. Here, we ...Ribosome assembly in eukaryotes requires approximately 200 essential assembly factors (AFs) and occurs through ordered events that initiate in the nucleolus and culminate in the cytoplasm. Here, we present the electron cryo-microscopy (cryo-EM) structure of a late cytoplasmic 40S ribosome assembly intermediate from Saccharomyces cerevisiae at 18 angstrom resolution. We obtained cryo-EM reconstructions of preribosomal complexes lacking individual components to define the positions of all seven AFs bound to this intermediate. These late-binding AFs are positioned to prevent each step in the translation initiation pathway. Together, they obstruct the binding sites for initiation factors, prevent the opening of the messenger RNA channel, block 60S subunit joining, and disrupt the decoding site. These redundant mechanisms probably ensure that pre-40S particles do not enter the translation pathway, which would result in their rapid degradation. | |||||||||
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_1927.map.gz | 11.6 MB | EMDB map data format | |
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Header (meta data) | emd-1927-v30.xml emd-1927.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | EMD-1927.png | 82 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1927 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1927 | 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_1927.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | surface render of wild type Pre-40s map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.24 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 : S. cerevisiae pre-40S ribosomal particle purified by Rio2-TAP
Entire | Name: S. cerevisiae pre-40S ribosomal particle purified by Rio2-TAP |
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Components |
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-Supramolecule #1000: S. cerevisiae pre-40S ribosomal particle purified by Rio2-TAP
Supramolecule | Name: S. cerevisiae pre-40S ribosomal particle purified by Rio2-TAP type: sample / ID: 1000 / Details: monodisperse / Number unique components: 1 |
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Molecular weight | Theoretical: 1.6 MDa |
-Supramolecule #1: pre-40s
Supramolecule | Name: pre-40s / type: complex / ID: 1 / Name.synonym: pre-40s / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers' yeast |
Molecular weight | Theoretical: 1.6 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 Details: 50mM Tris-CL, 100mM NaCl, 10mM MgCl2, 0.075% NP40, 1mM imidazole, 2mM EGTA, 10mM BME |
Grid | Details: quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 85 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 66964 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: OTHER |
Temperature | Min: 89 K / Max: 89 K / Average: 89 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 135,000 times magnification |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 460 / Average electron dose: 16 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each micrograph |
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Final angle assignment | Details: EMAN convention |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Details: Final map was filtered to 18A resolution / Number images used: 11604 |
Details | manual particle selection |
-Atomic model buiding 1
Initial model | PDB ID: 3o2z |
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Software | Name: NAMD |
Details | Protocol: MDFF. manual docking of modified 3o2z followed by MDFF. see publication |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: CC |