[English] 日本語
Yorodumi- EMDB-2422: Molecular architecture of the 80S-eIF5B-Met-itRNAMet Eukaryotic T... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2422 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Molecular architecture of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex | |||||||||
Map data | Reconstruction of 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex with tRNA in the P/I-site and density for all four domains of eIF5B. | |||||||||
Sample |
| |||||||||
Keywords | Ribosome initiation complex / initiator factor eiF5B / cryo EM / single particle analysis | |||||||||
Function / homology | Function and homology information ribosome hibernation / triplex DNA binding / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / protein-synthesizing GTPase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway ...ribosome hibernation / triplex DNA binding / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / protein-synthesizing GTPase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / GDP-dissociation inhibitor activity / regulation of translational initiation / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / : / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / translational elongation / response to cycloheximide / telomeric DNA binding / mRNA destabilization / TOR signaling / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / positive regulation of protein kinase activity / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / translation initiation factor binding / maturation of SSU-rRNA / translation repressor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / translational initiation / : / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to amino acid starvation / ribosome assembly / telomere maintenance / translation initiation factor activity / ribosomal large subunit biogenesis / cytosolic ribosome assembly / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cytoplasmic stress granule / small ribosomal subunit rRNA binding / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / negative regulation of translation / ribosome / rRNA binding / protein ubiquitination / structural constituent of ribosome / translation / G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / response to antibiotic / negative regulation of gene expression / GTPase activity / mRNA binding / ubiquitin protein ligase binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 6.6 Å | |||||||||
Authors | Fernandez IS / Bai XC / Hussain T / Kelley AC / Lorsch JR / Ramakrishnan V / Scheres SHW | |||||||||
Citation | Journal: Science / Year: 2013 Title: Molecular architecture of a eukaryotic translational initiation complex. Authors: Israel S Fernández / Xiao-Chen Bai / Tanweer Hussain / Ann C Kelley / Jon R Lorsch / V Ramakrishnan / Sjors H W Scheres / Abstract: The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start ...The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2422.map.gz | 49.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2422-v30.xml emd-2422.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | EMD-2422.jpg | 116.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2422 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2422 | HTTPS FTP |
-Related structure data
Related structure data | 4v8zMC 2421C 4v8yC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2422.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex with tRNA in the P/I-site and density for all four domains of eIF5B. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Reconstruction of 80S-eIF5B-Met-itRNAMet Eukaryotic Translation I...
Entire | Name: Reconstruction of 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex with tRNA in the P/I-site and density for all four domains of eIF5B. |
---|---|
Components |
|
-Supramolecule #1000: Reconstruction of 80S-eIF5B-Met-itRNAMet Eukaryotic Translation I...
Supramolecule | Name: Reconstruction of 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex with tRNA in the P/I-site and density for all four domains of eIF5B. type: sample / ID: 1000 / Number unique components: 2 |
---|---|
Molecular weight | Experimental: 4.2 MDa / Theoretical: 4.2 MDa |
-Supramolecule #1: 80S-Met-itRNAMet Eukaryotic Translation Initiation Complex
Supramolecule | Name: 80S-Met-itRNAMet Eukaryotic Translation Initiation Complex type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Molecular weight | Experimental: 4.2 MDa / Theoretical: 4.2 MDa |
-Macromolecule #1: eiF5B
Macromolecule | Name: eiF5B / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
---|---|
Buffer | pH: 7.2 Details: 3mM Hepes-KOH, 6.6 mM Tris-acetate pH 7.2, 3 mM NH4Cl, 6.6 mM NH4-acetate, 48 mM K-acetate, 4 mM Mg-acetate, 2.4 mM DTT |
Staining | Type: NEGATIVE / Details: cryo-EM |
Grid | Details: Quantifoil grids (2/2) with 3 nm thin carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK II / Method: Blot 2.5 seconds before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 79096 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.9 µm / Nominal defocus min: 1.9 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Temperature | Min: 80 K / Max: 90 K / Average: 85 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification |
Date | Jan 15, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 1012 / Average electron dose: 16 e/Å2 Details: Every image is the average of 16 frames recorded by the direct electron detector |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION Details: Use a newly developed statistical movie processing approach to compensate for beam-induced movement. Number images used: 5143 |
Details | Use a newly developed statistical movie processing approach to compensate for beam-induced movement. Use a newly developed statistical movie processing to compensate for beam-induced movement. |