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Yorodumi- PDB-5mc6: Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex fro... -
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-Basic information
Entry | Database: PDB / ID: 5mc6 | ||||||
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Title | Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae | ||||||
Components |
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Keywords | RIBOSOME / cryo-EM / RNA / helicase | ||||||
Function / homology | Function and homology information positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / mRNA decay by 3' to 5' exoribonuclease / Ski complex / 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 cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / mRNA decay by 3' to 5' exoribonuclease / Ski complex / 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 / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / reciprocal meiotic recombination / 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) / preribosome, small subunit precursor / response to cycloheximide / nuclear chromosome / 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 / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / 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 / 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 / Ub-specific processing proteases / positive regulation of translational initiation / translation elongation factor activity / 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 / translation initiation factor 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 / regulation of translation / 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 / protein-containing complex assembly / defense response to virus / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5mc6.cif.gz | 5.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5mc6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5mc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mc6_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5mc6_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5mc6_validation.xml.gz | 389.8 KB | Display | |
Data in CIF | 5mc6_validation.cif.gz | 679.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/5mc6 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/5mc6 | HTTPS FTP |
-Related structure data
Related structure data | 3461MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 7 types, 7 molecules 2lmnBQBRBS
#1: RNA chain | Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: REF: 831416132 |
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#35: RNA chain | Mass: 10494.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
#36: RNA chain | Mass: 24378.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
#37: RNA chain | Mass: 24815.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
#83: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: REF: 831416132 |
#84: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: GenBank: 1039024045 |
#85: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: GenBank: 1102645687 |
+40S ribosomal protein ... , 31 types, 31 molecules ABCDEFGHIJKLMPQRSTUVWXYZabcdefg
-Protein , 8 types, 9 molecules NOhijkAOAZBT
#15: Protein | Mass: 17254.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P05759 | ||||||
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#16: Protein | Mass: 34841.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P38011 | ||||||
#38: Protein | Mass: 146259.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P35207, RNA helicase | ||||||
#39: Protein | Mass: 163922.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P17883 | ||||||
#40: Protein | Mass: 44283.527 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: Q02793 #55: Protein | | Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P0CH08 #66: Protein | | Mass: 17889.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Due to resolution, this protein was only built as a poly-ala model. The actual uL1 sequence can be obtained from Uniprot-ID P0CX43. We had the same situation with a previous deposition of ...Details: Due to resolution, this protein was only built as a poly-ala model. The actual uL1 sequence can be obtained from Uniprot-ID P0CX43. We had the same situation with a previous deposition of our group (PDB-ID 5GAK). Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) #86: Protein | | Mass: 17222.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P23301 |
+60S ribosomal protein ... , 40 types, 40 molecules AAABACADAEAFAGAHAIAJAKALAMANAPAQARASATAUAVAWAXAYBABBBCBDBEBF...
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae Type: RIBOSOME / Entity ID: #1-#87 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 3.6 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER/PALLADIUM / Grid type: Quantifoil R3/3 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 2.8 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 2 |
Image scans | Used frames/image: 1-10 |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31503 / Symmetry type: POINT |