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Yorodumi- EMDB-10398: Structure of yeast disome (di-ribosome) stalled on poly(A) tract. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10398 | |||||||||
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Title | Structure of yeast disome (di-ribosome) stalled on poly(A) tract. | |||||||||
Map data | Composite map of multi-body refined yeast disome (di-ribosome) collided on poly(A) tract mRNA. Filtered according to local resolution. | |||||||||
Sample |
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Function / homology | Function and homology information : / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / positive regulation of translational fidelity / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation ...: / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / positive regulation of translational fidelity / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / mRNA destabilization / 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 / 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / protein-RNA complex assembly / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / Ub-specific processing proteases / regulation of translational fidelity / positive regulation of protein kinase activity / ribosomal small subunit export from nucleus / 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) / ribosomal subunit export from nucleus / translation regulator activity / translational termination / 90S preribosome / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / cellular response to amino acid starvation / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / ribosomal large subunit assembly / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Tesina P / Buschauer R / Cheng J / Berninghausen O / Becker R / Beckmann R | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: EMBO J / Year: 2020 Title: Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts. Authors: Petr Tesina / Laura N Lessen / Robert Buschauer / Jingdong Cheng / Colin Chih-Chien Wu / Otto Berninghausen / Allen R Buskirk / Thomas Becker / Roland Beckmann / Rachel Green / Abstract: Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still ...Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall- and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes. | |||||||||
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_10398.map.gz | 96.2 MB | EMDB map data format | |
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Header (meta data) | emd-10398-v30.xml emd-10398.xml | 90 KB 90 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10398_fsc_1.xml emd_10398_fsc_2.xml | 14.2 KB 14.3 KB | Display Display | FSC data file |
Images | emd_10398.png | 241.9 KB | ||
Others | emd_10398_additional_1.map.gz emd_10398_additional_2.map.gz | 140.7 MB 140.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10398 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10398 | HTTPS FTP |
-Related structure data
Related structure data | 6t83MC 6t4qC 6t7iC 6t7tC 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_10398.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of multi-body refined yeast disome (di-ribosome) collided on poly(A) tract mRNA. Filtered according to local resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Additional map: Individually refined body of the second colliding yeast...
File | emd_10398_additional_1.map | ||||||||||||
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Annotation | Individually refined body of the second colliding yeast 80S ribosome of the disome stalled on the poly(A) tract. Filtered according to local resolution. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Individually refined body of the first stalling yeast...
File | emd_10398_additional_2.map | ||||||||||||
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Annotation | Individually refined body of the first stalling yeast 80S ribosome of the disome stalled on the poly(A) tract. Filtered according to local resolution. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : yeast disome stalled on poly(A) tract
+Supramolecule #1: yeast disome stalled on poly(A) tract
+Macromolecule #1: 18S rRNA
+Macromolecule #35: 5S rRNA
+Macromolecule #36: 5.8S rRNA
+Macromolecule #78: 25S rRNA
+Macromolecule #79: tRNA
+Macromolecule #2: 40S ribosomal protein S0-A
+Macromolecule #3: 40S ribosomal protein S1-A
+Macromolecule #4: 40S ribosomal protein S15
+Macromolecule #5: 40S ribosomal protein S2
+Macromolecule #6: 40S ribosomal protein S3
+Macromolecule #7: 40S ribosomal protein S4-A
+Macromolecule #8: Rps5p
+Macromolecule #9: 40S ribosomal protein S6-A
+Macromolecule #10: 40S ribosomal protein S7-A
+Macromolecule #11: 40S ribosomal protein S8-A
+Macromolecule #12: 40S ribosomal protein S9-A
+Macromolecule #13: 40S ribosomal protein S10-A
+Macromolecule #14: 40S ribosomal protein S11-A
+Macromolecule #15: 40S ribosomal protein S12
+Macromolecule #16: 40S ribosomal protein S13
+Macromolecule #17: 40S ribosomal protein S14-A
+Macromolecule #18: 40S ribosomal protein S16-A
+Macromolecule #19: 40S ribosomal protein S17-B
+Macromolecule #20: 40S ribosomal protein S18-A
+Macromolecule #21: 40S ribosomal protein S19-A
+Macromolecule #22: 40S ribosomal protein S20
+Macromolecule #23: 40S ribosomal protein S21-A
+Macromolecule #24: 40S ribosomal protein S22-A
+Macromolecule #25: 40S ribosomal protein S23-A
+Macromolecule #26: 40S ribosomal protein S24-A
+Macromolecule #27: 40S ribosomal protein S25-A
+Macromolecule #28: 40S ribosomal protein S26-A
+Macromolecule #29: 40S ribosomal protein S27-A
+Macromolecule #30: 40S ribosomal protein S29-A
+Macromolecule #31: 40S ribosomal protein S30-A
+Macromolecule #32: Ubiquitin-40S ribosomal protein S31
+Macromolecule #33: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #34: 40S ribosomal protein S28-B
+Macromolecule #37: 60S ribosomal protein L2-A
+Macromolecule #38: 60S ribosomal protein L3
+Macromolecule #39: 60S ribosomal protein L4-A
+Macromolecule #40: 60S ribosomal protein L5
+Macromolecule #41: 60S ribosomal protein L6-A
+Macromolecule #42: 60S ribosomal protein L7-A
+Macromolecule #43: 60S ribosomal protein L8-A
+Macromolecule #44: 60S ribosomal protein L9-A
+Macromolecule #45: 60S ribosomal protein L10
+Macromolecule #46: 60S ribosomal protein L11-A
+Macromolecule #47: 60S ribosomal protein L13-A
+Macromolecule #48: 60S ribosomal protein L14-A
+Macromolecule #49: 60S ribosomal protein L15-A
+Macromolecule #50: 60S ribosomal protein L16-A
+Macromolecule #51: 60S ribosomal protein L17-A
+Macromolecule #52: 60S ribosomal protein L18-A
+Macromolecule #53: 60S ribosomal protein L19-A
+Macromolecule #54: 60S ribosomal protein L20-A
+Macromolecule #55: 60S ribosomal protein L21-A
+Macromolecule #56: 60S ribosomal protein L22-A
+Macromolecule #57: 60S ribosomal protein L23-A
+Macromolecule #58: 60S ribosomal protein L24-A
+Macromolecule #59: 60S ribosomal protein L25
+Macromolecule #60: 60S ribosomal protein L26-A
+Macromolecule #61: 60S ribosomal protein L27-A
+Macromolecule #62: 60S ribosomal protein L28
+Macromolecule #63: 60S ribosomal protein L29
+Macromolecule #64: 60S ribosomal protein L30
+Macromolecule #65: 60S ribosomal protein L31-A
+Macromolecule #66: 60S ribosomal protein L32
+Macromolecule #67: 60S ribosomal protein L33-A
+Macromolecule #68: 60S ribosomal protein L34-A
+Macromolecule #69: 60S ribosomal protein L35-A
+Macromolecule #70: 60S ribosomal protein L36-A
+Macromolecule #71: 60S ribosomal protein L37-A
+Macromolecule #72: 60S ribosomal protein L38
+Macromolecule #73: 60S ribosomal protein L39
+Macromolecule #74: Ubiquitin-60S ribosomal protein L40
+Macromolecule #75: 60S ribosomal protein L41-A
+Macromolecule #76: 60S ribosomal protein L42-A
+Macromolecule #77: 60S ribosomal protein L43-A
+Macromolecule #80: 60S acidic ribosomal protein P0
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |