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Yorodumi- EMDB-4474: Cryo-EM structure of the mRNA translating and degrading yeast 80S... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4474 | |||||||||
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Title | Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribosome / stalling / TRANSLATION / nuclease / exoribonuclease / Xrn1 | |||||||||
Function / homology | Function and homology information nuclear-transcribed mRNA catabolic process, 5'-3' exonucleolytic nonsense-mediated decay / eisosome membrane domain/MCC / sno(s)RNA processing / nuclear-transcribed mRNA catabolic process, no-go decay / karyogamy / NAD-cap decapping / eukaryotic initiation factor 4G binding / 5'-3' RNA exonuclease activity / tRNA decay / rRNA catabolic process ...nuclear-transcribed mRNA catabolic process, 5'-3' exonucleolytic nonsense-mediated decay / eisosome membrane domain/MCC / sno(s)RNA processing / nuclear-transcribed mRNA catabolic process, no-go decay / karyogamy / NAD-cap decapping / eukaryotic initiation factor 4G binding / 5'-3' RNA exonuclease activity / tRNA decay / rRNA catabolic process / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / traversing start control point of mitotic cell cycle / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / RMTs methylate histone arginines / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / cellular response to nitrogen starvation / regulation of telomere maintenance / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / preribosome, small subunit precursor / 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 / negative regulation of macroautophagy / 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 / nuclear-transcribed mRNA catabolic process / 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 / positive regulation of transcription initiation by RNA polymerase II / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / Ub-specific processing proteases / protein-RNA complex assembly / 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 / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / rescue of stalled ribosome / 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 / positive regulation of transcription elongation by RNA polymerase II / macroautophagy / protein kinase C binding / P-body / 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 / ribosome binding / ribosomal small subunit assembly / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / microtubule / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Tesina P / Heckel E | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structure of the 80S ribosome-Xrn1 nuclease complex. Authors: Petr Tesina / Elisabeth Heckel / Jingdong Cheng / Micheline Fromont-Racine / Robert Buschauer / Lukas Kater / Birgitta Beatrix / Otto Berninghausen / Alain Jacquier / Thomas Becker / Roland Beckmann / Abstract: Messenger RNA (mRNA) homeostasis represents an essential part of gene expression, in which the generation of mRNA by RNA polymerase is counter-balanced by its degradation by nucleases. The conserved ...Messenger RNA (mRNA) homeostasis represents an essential part of gene expression, in which the generation of mRNA by RNA polymerase is counter-balanced by its degradation by nucleases. The conserved 5'-to-3' exoribonuclease Xrn1 has a crucial role in eukaryotic mRNA homeostasis by degrading decapped or cleaved mRNAs post-translationally and, more surprisingly, also co-translationally. Here we report that active Xrn1 can directly and specifically interact with the translation machinery. A cryo-electron microscopy structure of a programmed Saccharomyces cerevisiae 80S ribosome-Xrn1 nuclease complex reveals how the conserved core of Xrn1 enables binding at the mRNA exit site of the ribosome. This interface provides a conduit for channelling of the mRNA from the ribosomal decoding site directly into the active center of the nuclease, thus separating mRNA decoding from degradation by only 17 ± 1 nucleotides. These findings explain how rapid 5'-to-3' mRNA degradation is coupled efficiently to its final round of mRNA translation. | |||||||||
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_4474.map.gz | 142.7 MB | EMDB map data format | |
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Header (meta data) | emd-4474-v30.xml emd-4474.xml | 110 KB 110 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4474_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_4474.png | 117.7 KB | ||
Filedesc metadata | emd-4474.cif.gz | 19.4 KB | ||
Others | emd_4474_additional.map.gz | 142.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4474 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4474 | HTTPS FTP |
-Validation report
Summary document | emd_4474_validation.pdf.gz | 548.1 KB | Display | EMDB validaton report |
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Full document | emd_4474_full_validation.pdf.gz | 547.7 KB | Display | |
Data in XML | emd_4474_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_4474_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4474 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4474 | HTTPS FTP |
-Related structure data
Related structure data | 6q8yMC 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_4474.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Additional map: Focus-refined map using soft mask around Xrn1. Local...
File | emd_4474_additional.map | ||||||||||||
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Annotation | Focus-refined map using soft mask around Xrn1. Local resolution filtered. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yeast 80S ribosome in complex with the Xrn11 exoribonuclease obta...
+Supramolecule #1: Yeast 80S ribosome in complex with the Xrn11 exoribonuclease obta...
+Supramolecule #2: ribosome
+Supramolecule #3: mRNA
+Supramolecule #4: 5'-3' exoribonuclease Xrn1
+Supramolecule #5: P-site tRNA
+Supramolecule #6: E-site tRNA
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #34: mRNA
+Macromolecule #35: P-site tRNA
+Macromolecule #36: E-site tRNA
+Macromolecule #54: 25S ribosomal RNA
+Macromolecule #55: 5S ribosomal RNA
+Macromolecule #56: 5.8S ribosomal RNA
+Macromolecule #2: 60S ribosomal protein L8-A
+Macromolecule #3: 60S ribosomal protein L23-A
+Macromolecule #4: 60S ribosomal protein L36-A
+Macromolecule #5: 60S ribosomal protein L9-A
+Macromolecule #6: 60S ribosomal protein L24-A
+Macromolecule #7: 60S ribosomal protein L37-A
+Macromolecule #8: 60S ribosomal protein L11-B
+Macromolecule #9: 60S ribosomal protein L25
+Macromolecule #10: 60S ribosomal protein L38
+Macromolecule #11: 60S ribosomal protein L13-A
+Macromolecule #12: 60S ribosomal protein L26-A
+Macromolecule #13: 60S ribosomal protein L39
+Macromolecule #14: 60S ribosomal protein L14-A
+Macromolecule #15: 60S ribosomal protein L27-A
+Macromolecule #16: Ubiquitin-60S ribosomal protein L40
+Macromolecule #17: 60S ribosomal protein L42-A
+Macromolecule #18: 60S ribosomal protein L15-A
+Macromolecule #19: 60S ribosomal protein L28
+Macromolecule #20: 60S ribosomal protein L41-B
+Macromolecule #21: 60S ribosomal protein L43-A
+Macromolecule #22: 60S ribosomal protein L16-A
+Macromolecule #23: 60S ribosomal protein L29
+Macromolecule #24: 60S ribosomal protein L2-A
+Macromolecule #25: 60S ribosomal protein L17-A
+Macromolecule #26: 40S ribosomal protein S21-A
+Macromolecule #27: 40S ribosomal protein S22-A
+Macromolecule #28: 40S ribosomal protein S23-A
+Macromolecule #29: 40S ribosomal protein S24-A
+Macromolecule #30: 40S ribosomal protein S26-B
+Macromolecule #31: 40S ribosomal protein S27-A
+Macromolecule #32: 40S ribosomal protein S30-A
+Macromolecule #33: 5'-3' exoribonuclease 1
+Macromolecule #37: 60S ribosomal protein L30
+Macromolecule #38: 60S ribosomal protein L3
+Macromolecule #39: 60S ribosomal protein L18-A
+Macromolecule #40: 60S ribosomal protein L31-A
+Macromolecule #41: 60S ribosomal protein L10
+Macromolecule #42: 60S ribosomal protein L4-A
+Macromolecule #43: 60S ribosomal protein L19-A
+Macromolecule #44: 60S ribosomal protein L32
+Macromolecule #45: 60S ribosomal protein L20-A
+Macromolecule #46: 60S ribosomal protein L5
+Macromolecule #47: 60S ribosomal protein L21-A
+Macromolecule #48: 60S ribosomal protein L33-A
+Macromolecule #49: 60S ribosomal protein L22-A
+Macromolecule #50: 60S ribosomal protein L6-A
+Macromolecule #51: 60S ribosomal protein L34-A
+Macromolecule #52: 60S ribosomal protein L7-A
+Macromolecule #53: 60S ribosomal protein L35-A
+Macromolecule #57: 40S ribosomal protein S3
+Macromolecule #58: Rps5p
+Macromolecule #59: 40S ribosomal protein S10-A
+Macromolecule #60: 40S ribosomal protein S12
+Macromolecule #61: 40S ribosomal protein S15
+Macromolecule #62: 40S ribosomal protein S16-A
+Macromolecule #63: 40S ribosomal protein S17-A
+Macromolecule #64: 40S ribosomal protein S18-A
+Macromolecule #65: 40S ribosomal protein S20
+Macromolecule #66: 40S ribosomal protein S25-A
+Macromolecule #67: 40S ribosomal protein S28-A
+Macromolecule #68: 40S ribosomal protein S29-A
+Macromolecule #69: Ubiquitin-40S ribosomal protein S31
+Macromolecule #70: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #71: 40S ribosomal protein S0-A
+Macromolecule #72: 40S ribosomal protein S1-A
+Macromolecule #73: 40S ribosomal protein S2
+Macromolecule #74: 40S ribosomal protein S4-A
+Macromolecule #75: 40S ribosomal protein S6-A
+Macromolecule #76: 40S ribosomal protein S7-A
+Macromolecule #77: 40S ribosomal protein S8-A
+Macromolecule #78: 40S ribosomal protein S9-A
+Macromolecule #79: 40S ribosomal protein S11-A
+Macromolecule #80: 40S ribosomal protein S13
+Macromolecule #81: 40S ribosomal protein S14-B
+Macromolecule #82: 40S ribosomal protein S19-A
+Macromolecule #83: ZINC ION
+Macromolecule #84: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 II (4k x 4k) / Average electron dose: 2.5 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 |