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Yorodumi- EMDB-10537: Yeast 80S ribosome in complex with eIF5A and decoding A-site and ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10537 | |||||||||
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Title | Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. | |||||||||
Map data | Cryo-EM density of the yeast 80S ribosome in complex with eIF5A and A-site and P-site tRNAs. Filtered according to local resolution. | |||||||||
Sample |
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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 / 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 / RMTs methylate histone arginines ...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 / 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 / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / hexon binding / 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 / 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) / Ribosomal scanning and start codon recognition / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / protein-RNA complex assembly / positive regulation of translational initiation / translation elongation factor activity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / translation initiation factor activity / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / viral capsid / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / host cell nucleus / nucleolus / perinuclear region of cytoplasm / mitochondrion Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Buschauer R / Cheng J / Berninghausen O / Tesina P / Becker T / Beckmann R | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Science / Year: 2020 Title: The Ccr4-Not complex monitors the translating ribosome for codon optimality. Authors: Robert Buschauer / Yoshitaka Matsuo / Takato Sugiyama / Ying-Hsin Chen / Najwa Alhusaini / Thomas Sweet / Ken Ikeuchi / Jingdong Cheng / Yasuko Matsuki / Risa Nobuta / Andrea Gilmozzi / Otto ...Authors: Robert Buschauer / Yoshitaka Matsuo / Takato Sugiyama / Ying-Hsin Chen / Najwa Alhusaini / Thomas Sweet / Ken Ikeuchi / Jingdong Cheng / Yasuko Matsuki / Risa Nobuta / Andrea Gilmozzi / Otto Berninghausen / Petr Tesina / Thomas Becker / Jeff Coller / Toshifumi Inada / Roland Beckmann / Abstract: Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA ...Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability. | |||||||||
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_10537.map.gz | 235.1 MB | EMDB map data format | |
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Header (meta data) | emd-10537-v30.xml emd-10537.xml | 89.2 KB 89.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10537_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_10537.png | 89.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10537 | HTTPS FTP |
-Validation report
Summary document | emd_10537_validation.pdf.gz | 280.2 KB | Display | EMDB validaton report |
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Full document | emd_10537_full_validation.pdf.gz | 279.4 KB | Display | |
Data in XML | emd_10537_validation.xml.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10537 | HTTPS FTP |
-Related structure data
Related structure data | 6tnuMC 6tb3C 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_10537.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM density of the yeast 80S ribosome in complex with eIF5A and A-site and P-site tRNAs. Filtered according to local resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Yeast 80S ribosome in complex with eIF5A programed by A-site and ...
+Supramolecule #1: Yeast 80S ribosome in complex with eIF5A programed by A-site and ...
+Macromolecule #1: 18S rRNA
+Macromolecule #2: mRNA
+Macromolecule #24: P-site tRNA
+Macromolecule #37: A-site tRNA
+Macromolecule #38: 25S rRNA
+Macromolecule #39: 5S rRNA
+Macromolecule #40: 5.8S rRNA
+Macromolecule #3: 40S ribosomal protein S0-A
+Macromolecule #4: 40S ribosomal protein S1-A
+Macromolecule #5: 40S ribosomal protein S15
+Macromolecule #6: 40S ribosomal protein S2
+Macromolecule #7: 40S ribosomal protein S3
+Macromolecule #8: 40S ribosomal protein S4-A
+Macromolecule #9: Rps5p
+Macromolecule #10: 40S ribosomal protein S6-A
+Macromolecule #11: 40S ribosomal protein S7-A
+Macromolecule #12: 40S ribosomal protein S8
+Macromolecule #13: 40S ribosomal protein S9-A
+Macromolecule #14: 40S ribosomal protein S10-A
+Macromolecule #15: 40S ribosomal protein S11-A
+Macromolecule #16: 40S ribosomal protein S12
+Macromolecule #17: 40S ribosomal protein S13
+Macromolecule #18: 40S ribosomal protein S14-B
+Macromolecule #19: 40S ribosomal protein S16-A
+Macromolecule #20: 40S ribosomal protein S17-B
+Macromolecule #21: 40S ribosomal protein S18-A
+Macromolecule #22: 40S ribosomal protein S19-A
+Macromolecule #23: 40S ribosomal protein S20
+Macromolecule #25: 40S ribosomal protein S21-A
+Macromolecule #26: 40S ribosomal protein S22-A
+Macromolecule #27: 40S ribosomal protein S23-A
+Macromolecule #28: 40S ribosomal protein S24-A
+Macromolecule #29: 40S ribosomal protein S25-A
+Macromolecule #30: 40S ribosomal protein S26-B
+Macromolecule #31: 40S ribosomal protein S27-A
+Macromolecule #32: 40S ribosomal protein S29-A
+Macromolecule #33: 40S ribosomal protein S30-A
+Macromolecule #34: Ubiquitin-40S ribosomal protein S31
+Macromolecule #35: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #36: 40S ribosomal protein S28-A
+Macromolecule #41: 60S ribosomal protein L2-A
+Macromolecule #42: 60S ribosomal protein L3
+Macromolecule #43: 60S ribosomal protein L4-A
+Macromolecule #44: 60S ribosomal protein L5
+Macromolecule #45: 60S ribosomal protein L6-B
+Macromolecule #46: 60S ribosomal protein L7-A
+Macromolecule #47: 60S ribosomal protein L8-A
+Macromolecule #48: 60S ribosomal protein L9-A
+Macromolecule #49: 60S ribosomal protein L10
+Macromolecule #50: 60S ribosomal protein L11-B
+Macromolecule #51: 60S ribosomal protein L13-A
+Macromolecule #52: 60S ribosomal protein L14-A
+Macromolecule #53: 60S ribosomal protein L15-A
+Macromolecule #54: 60S ribosomal protein L16-A
+Macromolecule #55: 60S ribosomal protein L17-A
+Macromolecule #56: 60S ribosomal protein L18-A
+Macromolecule #57: 60S ribosomal protein L19-A
+Macromolecule #58: 60S ribosomal protein L20-A
+Macromolecule #59: 60S ribosomal protein L21-A
+Macromolecule #60: 60S ribosomal protein L22-A
+Macromolecule #61: 60S ribosomal protein L23-A
+Macromolecule #62: 60S ribosomal protein L24-A
+Macromolecule #63: 60S ribosomal protein L25
+Macromolecule #64: 60S ribosomal protein L26-A
+Macromolecule #65: 60S ribosomal protein L27-A
+Macromolecule #66: 60S ribosomal protein L28
+Macromolecule #67: 60S ribosomal protein L29
+Macromolecule #68: 60S ribosomal protein L30
+Macromolecule #69: 60S ribosomal protein L31-A
+Macromolecule #70: 60S ribosomal protein L32
+Macromolecule #71: 60S ribosomal protein L33-A
+Macromolecule #72: 60S ribosomal protein L34-A
+Macromolecule #73: 60S ribosomal protein L35-A
+Macromolecule #74: 60S ribosomal protein L36-A
+Macromolecule #75: 60S ribosomal protein L37-A
+Macromolecule #76: 60S ribosomal protein L38
+Macromolecule #77: 60S ribosomal protein L39
+Macromolecule #78: Ubiquitin-60S ribosomal protein L40
+Macromolecule #79: 60S ribosomal protein L41-A
+Macromolecule #80: 60S ribosomal protein L42-A
+Macromolecule #81: 60S ribosomal protein L43-A
+Macromolecule #82: Eukaryotic translation initiation factor 5A-1
+Macromolecule #83: 60S ribosomal protein L1
+Macromolecule #84: ZINC ION
+Macromolecule #85: SPERMIDINE
+Macromolecule #86: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |