+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3227 | |||||||||
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Title | Cryo-EM map of a native 80S-ribosome-eIF-5A complex | |||||||||
Map data | Ribosome reconstruction | |||||||||
Sample |
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Keywords | Translation | |||||||||
Function / homology | Function and homology information positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane ...positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / positive regulation of translational initiation / translation elongation factor activity / translational termination / translation initiation factor activity / maturation of LSU-rRNA / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / mitochondrion / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.88 Å | |||||||||
Authors | Schmidt C / Becker T / Heuer A / Braunger K / Shanmuganathan V / Pech M / m Berninghausen O / Wilson D / Beckmann R | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2016 Title: Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome. Authors: Christian Schmidt / Thomas Becker / André Heuer / Katharina Braunger / Vivekanandan Shanmuganathan / Markus Pech / Otto Berninghausen / Daniel N Wilson / Roland Beckmann / Abstract: During protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5A (a/eIF-5A) and in bacteria by the ...During protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5A (a/eIF-5A) and in bacteria by the homologous protein EF-P. While a structure of EF-P bound to the 70S ribosome exists, structural insight into eIF-5A on the 80S ribosome has been lacking. Here we present a cryo-electron microscopy reconstruction of eIF-5A bound to the yeast 80S ribosome at 3.9 Å resolution. The structure reveals that the unique and functionally essential post-translational hypusine modification reaches toward the peptidyltransferase center of the ribosome, where the hypusine moiety contacts A76 of the CCA-end of the P-site tRNA. These findings would support a model whereby eIF-5A stimulates peptide bond formation on polyproline-stalled ribosomes by stabilizing and orienting the CCA-end of the P-tRNA, rather than by directly contributing to the catalysis. | |||||||||
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_3227.map.gz | 179.3 MB | EMDB map data format | |
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Header (meta data) | emd-3227-v30.xml emd-3227.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | EMD_3227.jpg | 160.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3227 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3227 | HTTPS FTP |
-Validation report
Summary document | emd_3227_validation.pdf.gz | 325.7 KB | Display | EMDB validaton report |
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Full document | emd_3227_full_validation.pdf.gz | 324.8 KB | Display | |
Data in XML | emd_3227_validation.xml.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3227 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3227 | HTTPS FTP |
-Related structure data
Related structure data | 5gakMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_3227.map.gz / Format: CCP4 / Size: 188.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ribosome reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 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 : Native 80S ribosome-eIF-5A complex from yeast
Entire | Name: Native 80S ribosome-eIF-5A complex from yeast |
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Components |
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-Supramolecule #1000: Native 80S ribosome-eIF-5A complex from yeast
Supramolecule | Name: Native 80S ribosome-eIF-5A complex from yeast / type: sample / ID: 1000 / Details: Sample was obtained from a native pullout / Oligomeric state: One ribosome binds one eIF-5A molecule / Number unique components: 2 |
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-Supramolecule #1: Ribosome
Supramolecule | Name: Ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast / Location in cell: Cytoplasm |
-Macromolecule #1: eIF-5A
Macromolecule | Name: eIF-5A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 170 KDa |
Sequence | UniProtKB: Eukaryotic translation initiation factor 5A-1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Details: 20 mM HEPES, pH7.4, 100 mM KOAc, 10 mM MgCl2, 0.01 mg/ml Cycloheximide |
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Grid | Details: Quantifoil R3/3 grids with 2 nM carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Feb 25, 2015 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 3786 Details: The data was provided with the semi-automated software EPU (FEI Company) with a dose of 2.4 electrons per frame for 13 frames in total. The frames were aligned with the Motion Correction software Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Computational sorting and classification was done in SPIDER, movie processing and high resolution refinement was done with RELION |
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CTF correction | Details: Each Particle |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: OTHER / Software - Name: SIGNATURE, CTFFIND3, SPIDER, RELION / Number images used: 62532 |