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Yorodumi- EMDB-3461: Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex fro... -
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-Basic information
Entry | Database: EMDB / ID: EMD-3461 | |||||||||
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Title | Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae | |||||||||
Map data | Native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae | |||||||||
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 / Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / positive regulation of translational termination / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : ...positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / positive regulation of translational termination / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / 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 / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / reciprocal meiotic recombination / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / GDP-dissociation inhibitor activity / : / 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 / 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 / preribosome, small subunit precursor / translational elongation / response to cycloheximide / nuclear chromosome / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / mRNA catabolic process / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / protein-RNA complex assembly / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / positive regulation of translational initiation / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 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) / regulation of translational fidelity / positive regulation of protein kinase activity / translation elongation factor activity / rescue of stalled ribosome / translational termination / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / ribosome assembly / translation initiation factor activity / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / macroautophagy / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / protein tag activity / ribosomal small subunit assembly / ribosomal large subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / regulation of translation / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / protein-containing complex assembly / defense response to virus / negative regulation of translation / RNA helicase activity / rRNA binding / protein ubiquitination / RNA helicase / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Schmidt C / Kowalinski E / Shanmuganathan V / Defenouillere Q / Braunger K / Heuer A / Pech M / Namane A / Berninghausen O / Fromont-Racine M ...Schmidt C / Kowalinski E / Shanmuganathan V / Defenouillere Q / Braunger K / Heuer A / Pech M / Namane A / Berninghausen O / Fromont-Racine M / Jacquier A / Conti E / Becker T / Beckmann R | |||||||||
Citation | Journal: Science / Year: 2016 Title: The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Authors: Christian Schmidt / Eva Kowalinski / Vivekanandan Shanmuganathan / Quentin Defenouillère / Katharina Braunger / André Heuer / Markus Pech / Abdelkader Namane / Otto Berninghausen / ...Authors: Christian Schmidt / Eva Kowalinski / Vivekanandan Shanmuganathan / Quentin Defenouillère / Katharina Braunger / André Heuer / Markus Pech / Abdelkader Namane / Otto Berninghausen / Micheline Fromont-Racine / Alain Jacquier / Elena Conti / Thomas Becker / Roland Beckmann / Abstract: Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski ...Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski complex directly associates with 80S ribosomes presenting a short mRNA 3' overhang. We determined the structure of an endogenous ribosome-Ski complex using cryo-electron microscopy (EM) with a local resolution of the Ski complex ranging from 4 angstroms (Å) in the core to about 10 Å for intrinsically flexible regions. Ribosome binding displaces the autoinhibitory domain of the Ski2 helicase, positioning it in an open conformation near the ribosomal mRNA entry tunnel. We observe that the mRNA 3' overhang is threaded directly from the small ribosomal subunit to the helicase channel of Ski2, primed for ongoing exosome-mediated 3'-5' degradation. | |||||||||
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_3461.map.gz | 381.9 MB | EMDB map data format | |
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Header (meta data) | emd-3461-v30.xml emd-3461.xml | 99.1 KB 99.1 KB | Display Display | EMDB header |
Images | emd_3461.png | 38.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3461 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3461 | HTTPS FTP |
-Related structure data
Related structure data | 5mc6MC 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_3461.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae
+Supramolecule #1: Native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #35: mRNA
+Macromolecule #36: A-site tRNA
+Macromolecule #37: P-site tRNA
+Macromolecule #83: 25S ribosomal RNA
+Macromolecule #84: 5S ribosomal RNA
+Macromolecule #85: 5.8S ribosomal RNA
+Macromolecule #2: 40S ribosomal protein S3
+Macromolecule #3: 40S ribosomal protein S5
+Macromolecule #4: 40S ribosomal protein S10-A
+Macromolecule #5: 40S ribosomal protein S12
+Macromolecule #6: 40S ribosomal protein S15
+Macromolecule #7: 40S ribosomal protein S16-A
+Macromolecule #8: 40S ribosomal protein S17-B
+Macromolecule #9: 40S ribosomal protein S18-A
+Macromolecule #10: 40S ribosomal protein S19-A
+Macromolecule #11: 40S ribosomal protein S20
+Macromolecule #12: 40S ribosomal protein S25-A
+Macromolecule #13: 40S ribosomal protein S28-B
+Macromolecule #14: 40S ribosomal protein S29-A
+Macromolecule #15: Ubiquitin-40S ribosomal protein S31
+Macromolecule #16: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #17: 40S ribosomal protein S0-A
+Macromolecule #18: 40S ribosomal protein S1-A
+Macromolecule #19: 40S ribosomal protein S2
+Macromolecule #20: 40S ribosomal protein S4-A
+Macromolecule #21: 40S ribosomal protein S6-A
+Macromolecule #22: 40S ribosomal protein S7-A
+Macromolecule #23: 40S ribosomal protein S8-A
+Macromolecule #24: 40S ribosomal protein S9-A
+Macromolecule #25: 40S ribosomal protein S11-A
+Macromolecule #26: 40S ribosomal protein S13
+Macromolecule #27: 40S ribosomal protein S14-A
+Macromolecule #28: 40S ribosomal protein S21-A
+Macromolecule #29: 40S ribosomal protein S22-A
+Macromolecule #30: 40S ribosomal protein S23-A
+Macromolecule #31: 40S ribosomal protein S24-A
+Macromolecule #32: 40S ribosomal protein S26-A
+Macromolecule #33: 40S ribosomal protein S27-A
+Macromolecule #34: 40S ribosomal protein S30-A
+Macromolecule #38: Antiviral helicase SKI2
+Macromolecule #39: Superkiller protein 3
+Macromolecule #40: Antiviral protein SKI8
+Macromolecule #41: 60S ribosomal protein L8-A
+Macromolecule #42: 60S ribosomal protein L23-A
+Macromolecule #43: 60S ribosomal protein L36-A
+Macromolecule #44: 60S ribosomal protein L9-A
+Macromolecule #45: 60S ribosomal protein L24-A
+Macromolecule #46: 60S ribosomal protein L37-A
+Macromolecule #47: 60S ribosomal protein L11-A
+Macromolecule #48: 60S ribosomal protein L25
+Macromolecule #49: 60S ribosomal protein L38
+Macromolecule #50: 60S ribosomal protein L13-A
+Macromolecule #51: 60S ribosomal protein L26-A
+Macromolecule #52: 60S ribosomal protein L39
+Macromolecule #53: 60S ribosomal protein L14-A
+Macromolecule #54: 60S ribosomal protein L27-A
+Macromolecule #55: Ubiquitin-60S ribosomal protein L40
+Macromolecule #56: 60S ribosomal protein L42-A
+Macromolecule #57: 60S ribosomal protein L15-A
+Macromolecule #58: 60S ribosomal protein L28
+Macromolecule #59: 60S ribosomal protein L41-A
+Macromolecule #60: 60S ribosomal protein L43-A
+Macromolecule #61: 60S ribosomal protein L16-A
+Macromolecule #62: 60S ribosomal protein L29
+Macromolecule #63: 60S ribosomal protein L2-A
+Macromolecule #64: 60S ribosomal protein L17-A
+Macromolecule #65: 60S ribosomal protein L30
+Macromolecule #66: uL1
+Macromolecule #67: 60S ribosomal protein L3
+Macromolecule #68: 60S ribosomal protein L18-A
+Macromolecule #69: 60S ribosomal protein L31-A
+Macromolecule #70: 60S ribosomal protein L10
+Macromolecule #71: 60S ribosomal protein L4-A
+Macromolecule #72: 60S ribosomal protein L19-A
+Macromolecule #73: 60S ribosomal protein L32
+Macromolecule #74: 60S ribosomal protein L20-A
+Macromolecule #75: 60S ribosomal protein L5
+Macromolecule #76: 60S ribosomal protein L21-A
+Macromolecule #77: 60S ribosomal protein L33-A
+Macromolecule #78: 60S ribosomal protein L22-A
+Macromolecule #79: 60S ribosomal protein L6-A
+Macromolecule #80: 60S ribosomal protein L34-A
+Macromolecule #81: 60S ribosomal protein L7-A
+Macromolecule #82: 60S ribosomal protein L35-A
+Macromolecule #86: 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 Component:
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Grid | Model: Quantifoil R3/3 / Material: COPPER/PALLADIUM / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-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 / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Frames/image: 1-10 / Number grids imaged: 2 / Average electron dose: 2.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Startup model | Type of model: OTHER / Details: Yeast 80S ribosome |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 31503 |