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Yorodumi- EMDB-1922: Ribosome Assembly Factors Prevent Premature Translation Initiatio... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1922 | |||||||||
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Title | Ribosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates | |||||||||
Map data | Image of surface rendered view of Tsr1 recombinant protein | |||||||||
Sample |
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Keywords | pre-40S / Rio2-TAP / 40S intermediate | |||||||||
Function / homology | Function and homology information endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / preribosome, small subunit precursor / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTPase activity / nucleolus / GTP binding ...endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / preribosome, small subunit precursor / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / ribonucleoprotein complex binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GTPase activity / nucleolus / GTP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 30.0 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_1922.map.gz | 306.3 KB | EMDB map data format | |
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Header (meta data) | emd-1922-v30.xml emd-1922.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | EMD-1922.png | 24 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1922 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1922 | HTTPS FTP |
-Validation report
Summary document | emd_1922_validation.pdf.gz | 190.1 KB | Display | EMDB validaton report |
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Full document | emd_1922_full_validation.pdf.gz | 189.3 KB | Display | |
Data in XML | emd_1922_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1922 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1922 | 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_1922.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Image of surface rendered view of Tsr1 recombinant protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.16 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 : Recombinant Tsr1
Entire | Name: Recombinant Tsr1 |
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Components |
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-Supramolecule #1000: Recombinant Tsr1
Supramolecule | Name: Recombinant Tsr1 / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: 1 / Number unique components: 1 |
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Molecular weight | Theoretical: 91 KDa |
-Macromolecule #1: Tsr1
Macromolecule | Name: Tsr1 / type: protein_or_peptide / ID: 1 / Name.synonym: Tsr1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Molecular weight | Experimental: 91 KDa / Theoretical: 91 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: Ribosome biogenesis protein TSR1 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 50mM Tris-Cl 100mM NaCl 10mM MgCl2 |
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Staining | Type: NEGATIVE / Details: See publication for details. |
Grid | Details: Continuous carbon grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 200 / Average electron dose: 20 e/Å2 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 71138 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.1 µm |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER / Tilt angle max: 60 |