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Yorodumi- EMDB-10098: Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10098 | |||||||||
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Title | Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1 | |||||||||
Map data | Full map of the New1-80S complex at an avarage resolution of 3.28 A. | |||||||||
Sample |
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Function / homology | Function and homology information : / translation termination factor activity / regulation of translational termination / 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 / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling ...: / translation termination factor activity / regulation of translational termination / 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 / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / 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 / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / poly(A)+ mRNA export from nucleus / preribosome, small subunit precursor / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / ATPase-coupled transmembrane transporter activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / 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 / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / 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 / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / 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 / ATP hydrolysis activity / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||
Authors | Kasari V / Pochopien AA / Margus T / Murina V / Turnbull K / Zhou Y / Nissan T / Graf M / Novacek J / Atkinson GC ...Kasari V / Pochopien AA / Margus T / Murina V / Turnbull K / Zhou Y / Nissan T / Graf M / Novacek J / Atkinson GC / Johansson MJO / Wilson DN / Hauryliuk V | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2019 Title: A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling. Authors: Villu Kasari / Agnieszka A Pochopien / Tõnu Margus / Victoriia Murina / Kathryn Turnbull / Yang Zhou / Tracy Nissan / Michael Graf / Jiří Nováček / Gemma C Atkinson / Marcus J O ...Authors: Villu Kasari / Agnieszka A Pochopien / Tõnu Margus / Victoriia Murina / Kathryn Turnbull / Yang Zhou / Tracy Nissan / Michael Graf / Jiří Nováček / Gemma C Atkinson / Marcus J O Johansson / Daniel N Wilson / Vasili Hauryliuk / Abstract: Translation is controlled by numerous accessory proteins and translation factors. In the yeast Saccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ...Translation is controlled by numerous accessory proteins and translation factors. In the yeast Saccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ATPase eEF3. A closely related protein, New1, is encoded by a non-essential gene with cold sensitivity and ribosome assembly defect knock-out phenotypes. Since the exact molecular function of New1 is unknown, it is unclear if the ribosome assembly defect is direct, i.e. New1 is a bona fide assembly factor, or indirect, for instance due to a defect in protein synthesis. To investigate this, we employed yeast genetics, cryo-electron microscopy (cryo-EM) and ribosome profiling (Ribo-Seq) to interrogate the molecular function of New1. Overexpression of New1 rescues the inviability of a yeast strain lacking the otherwise strictly essential translation factor eEF3. The structure of the ATPase-deficient (EQ2) New1 mutant locked on the 80S ribosome reveals that New1 binds analogously to the ribosome as eEF3. Finally, Ribo-Seq analysis revealed that loss of New1 leads to ribosome queuing upstream of 3'-terminal lysine and arginine codons, including those genes encoding proteins of the cytoplasmic translational machinery. Our results suggest that New1 is a translation factor that fine-tunes the efficiency of translation termination or ribosome recycling. | |||||||||
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_10098.map.gz | 23.6 MB | EMDB map data format | |
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Header (meta data) | emd-10098-v30.xml emd-10098.xml | 107.8 KB 107.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10098_fsc.xml | 17.4 KB | Display | FSC data file |
Images | emd_10098.png | 257.1 KB | ||
Others | emd_10098_additional_1.map.gz emd_10098_additional_2.map.gz emd_10098_additional_3.map.gz emd_10098_half_map_1.map.gz emd_10098_half_map_2.map.gz | 14.1 MB 3.9 MB 8 MB 224.7 MB 224.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10098 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10098 | HTTPS FTP |
-Validation report
Summary document | emd_10098_validation.pdf.gz | 437.5 KB | Display | EMDB validaton report |
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Full document | emd_10098_full_validation.pdf.gz | 436.6 KB | Display | |
Data in XML | emd_10098_validation.xml.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10098 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10098 | HTTPS FTP |
-Related structure data
Related structure data | 6s47MC 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_10098.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full map of the New1-80S complex at an avarage resolution of 3.28 A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: None
File | emd_10098_additional_1.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_10098_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_10098_additional_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: First half-map of 3.28A full map.mrc
File | emd_10098_half_map_1.map | ||||||||||||
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Annotation | First half-map of 3.28A_full_map.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half-map of 3.28A full map.mrc
File | emd_10098_half_map_2.map | ||||||||||||
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Annotation | Second half-map of 3.28A_full_map.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : New1-80S Complex
+Supramolecule #1: New1-80S Complex
+Supramolecule #2: 80s ribosome
+Supramolecule #3: New1
+Macromolecule #1: 28S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #45: 18S rRNA (1707-MER)
+Macromolecule #4: 60S ribosomal protein L2-A
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4-A
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6-A
+Macromolecule #9: 60S ribosomal protein L7-A
+Macromolecule #10: 60S ribosomal protein L8-A
+Macromolecule #11: 60S ribosomal protein L9-A
+Macromolecule #12: 60S ribosomal protein L10
+Macromolecule #13: 60S ribosomal protein L11-B
+Macromolecule #14: 60S ribosomal protein L13-A
+Macromolecule #15: 60S ribosomal protein L14-A
+Macromolecule #16: 60S ribosomal protein L15-A
+Macromolecule #17: 60S ribosomal protein L16-A
+Macromolecule #18: 60S ribosomal protein L17-A
+Macromolecule #19: 60S ribosomal protein L18-A
+Macromolecule #20: 60S ribosomal protein L19-A
+Macromolecule #21: 60S ribosomal protein L20-A
+Macromolecule #22: 60S ribosomal protein L21-A
+Macromolecule #23: 60S ribosomal protein L22-A
+Macromolecule #24: 60S ribosomal protein L23-A
+Macromolecule #25: 60S ribosomal protein L24-A
+Macromolecule #26: 60S ribosomal protein L25
+Macromolecule #27: 60S ribosomal protein L26-A
+Macromolecule #28: 60S ribosomal protein L27-A
+Macromolecule #29: 60S ribosomal protein L28
+Macromolecule #30: 60S ribosomal protein L29
+Macromolecule #31: 60S ribosomal protein L30
+Macromolecule #32: 60S ribosomal protein L31-A
+Macromolecule #33: 60S ribosomal protein L32
+Macromolecule #34: 60S ribosomal protein L33-A
+Macromolecule #35: 60S ribosomal protein L34-A
+Macromolecule #36: 60S ribosomal protein L35-A
+Macromolecule #37: 60S ribosomal protein L36-A
+Macromolecule #38: 60S ribosomal protein L37-A
+Macromolecule #39: 60S ribosomal protein L38
+Macromolecule #40: 60S ribosomal protein L39
+Macromolecule #41: Ubiquitin-60S ribosomal protein L40
+Macromolecule #42: 60S ribosomal protein L41-B
+Macromolecule #43: 60S ribosomal protein L42-A
+Macromolecule #44: 60S ribosomal protein L43-A
+Macromolecule #46: 40S ribosomal protein S0-A
+Macromolecule #47: 40S ribosomal protein S1-A
+Macromolecule #48: 40S ribosomal protein S2
+Macromolecule #49: 40S ribosomal protein S3
+Macromolecule #50: 40S ribosomal protein S4-A
+Macromolecule #51: Rps5p
+Macromolecule #52: 40S ribosomal protein S6-A
+Macromolecule #53: 40S ribosomal protein S7-A
+Macromolecule #54: 40S ribosomal protein S8-A
+Macromolecule #55: 40S ribosomal protein S9-A
+Macromolecule #56: 40S ribosomal protein S10-A
+Macromolecule #57: 40S ribosomal protein S11-A
+Macromolecule #58: 40S ribosomal protein S12
+Macromolecule #59: 40S ribosomal protein S13
+Macromolecule #60: 40S ribosomal protein S14-A
+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 S19-A
+Macromolecule #66: 40S ribosomal protein S20
+Macromolecule #67: 40S ribosomal protein S21-A
+Macromolecule #68: 40S ribosomal protein S22-A
+Macromolecule #69: 40S ribosomal protein S23-A
+Macromolecule #70: 40S ribosomal protein S24-A
+Macromolecule #71: 40S ribosomal protein S25-A
+Macromolecule #72: 40S ribosomal protein S26-B
+Macromolecule #73: 40S ribosomal protein S27-A
+Macromolecule #74: 40S ribosomal protein S28-A
+Macromolecule #75: 40S ribosomal protein S29-A
+Macromolecule #76: 40S ribosomal protein S30-A
+Macromolecule #77: Ubiquitin-40S ribosomal protein S31
+Macromolecule #78: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #79: [NU+] prion formation protein 1
+Macromolecule #80: ADENOSINE-5'-TRIPHOSPHATE
-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-PROPANE |
-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: 45.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |