+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4140 | |||||||||
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Title | Nonstop ribosomal complex bound with Dom34 and Hbs1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | mRNA surveillance / ribosome | |||||||||
Function / homology | Function and homology information Eukaryotic Translation Elongation / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / 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 ...Eukaryotic Translation Elongation / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / HSF1 activation / 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 / ribosome disassembly / 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 / 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 / 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 / meiotic cell cycle / 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 / Neutrophil degranulation / RNA 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 / positive regulation of translation / translational initiation / macroautophagy / protein kinase C binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / cell division / negative regulation of gene expression / response to antibiotic / GTPase activity Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Hilal T / Yamamoto H | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Commun / Year: 2016 Title: Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution. Authors: Tarek Hilal / Hiroshi Yamamoto / Justus Loerke / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / Abstract: The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational ...The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational machinery. During ribosomal rescue, arrested ribosomes are specifically recognized by the conserved eukaryotic proteins Dom34 and Hbs1, to initiate their recycling. Here we solve the structure of Dom34 and Hbs1 bound to a yeast ribosome programmed with a nonstop mRNA at 3.3 Å resolution using cryo-electron microscopy. The structure shows that Domain N of Dom34 is inserted into the upstream mRNA-binding groove via direct stacking interactions with conserved nucleotides of 18S rRNA. It senses the absence of mRNA at the A-site and part of the mRNA entry channel by direct competition. Thus, our analysis establishes the structural foundation for the recognition of aberrantly stalled 80S ribosomes by the Dom34·Hbs1·GTP complex during Dom34-mediated mRNA surveillance pathways. | |||||||||
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_4140.map.gz | 143.7 MB | EMDB map data format | |
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Header (meta data) | emd-4140-v30.xml emd-4140.xml | 99 KB 99 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4140_fsc.xml | 17.1 KB | Display | FSC data file |
Images | emd_4140.png | 111.2 KB | ||
Filedesc metadata | emd-4140.cif.gz | 19.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4140 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4140 | HTTPS FTP |
-Validation report
Summary document | emd_4140_validation.pdf.gz | 298 KB | Display | EMDB validaton report |
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Full document | emd_4140_full_validation.pdf.gz | 297.1 KB | Display | |
Data in XML | emd_4140_validation.xml.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4140 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4140 | HTTPS FTP |
-Related structure data
Related structure data | 5m1jMC 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_4140.map.gz / Format: CCP4 / Size: 266.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.994 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 : Nonstop ribosomal complex bound with Dom34-Hbs1-GMPPNP
+Supramolecule #1: Nonstop ribosomal complex bound with Dom34-Hbs1-GMPPNP
+Macromolecule #1: Protein DOM34
+Macromolecule #2: 40S ribosomal protein S0-A
+Macromolecule #3: 40S ribosomal protein S26-B
+Macromolecule #4: 40S ribosomal protein S1-A
+Macromolecule #5: 40S ribosomal protein S27-A
+Macromolecule #6: 40S ribosomal protein S2
+Macromolecule #7: 40S ribosomal protein S28-B
+Macromolecule #8: 40S ribosomal protein S3
+Macromolecule #9: 40S ribosomal protein S29-A
+Macromolecule #10: 40S ribosomal protein S4-A
+Macromolecule #11: 40S ribosomal protein S30-A
+Macromolecule #12: 40S ribosomal protein S5
+Macromolecule #13: 40S ribosomal protein S6-A
+Macromolecule #14: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #15: 40S ribosomal protein S7-A
+Macromolecule #16: 40S ribosomal protein S8-A
+Macromolecule #17: 40S ribosomal protein S9-A
+Macromolecule #18: 40S ribosomal protein S10-A
+Macromolecule #19: 40S ribosomal protein S11-A
+Macromolecule #20: 40S ribosomal protein S12
+Macromolecule #21: 40S ribosomal protein S13
+Macromolecule #22: 40S ribosomal protein S14-A
+Macromolecule #23: 40S ribosomal protein S15
+Macromolecule #24: 40S ribosomal protein S16-A
+Macromolecule #25: 40S ribosomal protein S17-B
+Macromolecule #26: 40S ribosomal protein S18-A
+Macromolecule #27: 40S ribosomal protein S19-A
+Macromolecule #28: 40S ribosomal protein S20
+Macromolecule #29: 40S ribosomal protein S21-A
+Macromolecule #30: 40S ribosomal protein S22-A
+Macromolecule #31: 40S ribosomal protein S23-A
+Macromolecule #32: 40S ribosomal protein S24-A
+Macromolecule #33: 40S ribosomal protein S25-A
+Macromolecule #35: Ubiquitin-40S ribosomal protein S31
+Macromolecule #39: 60S ribosomal protein L28
+Macromolecule #40: 60S ribosomal protein L2-A
+Macromolecule #41: 60S ribosomal protein L29
+Macromolecule #42: 60S ribosomal protein L3
+Macromolecule #43: 60S ribosomal protein L30
+Macromolecule #44: 60S ribosomal protein L4-A
+Macromolecule #45: 60S ribosomal protein L5
+Macromolecule #46: 60S ribosomal protein L31-A
+Macromolecule #47: 60S ribosomal protein L32
+Macromolecule #48: 60S ribosomal protein L33-A
+Macromolecule #49: 60S ribosomal protein L7-A
+Macromolecule #50: 60S ribosomal protein L34-A
+Macromolecule #51: 60S ribosomal protein L8-A
+Macromolecule #52: 60S ribosomal protein L35-A
+Macromolecule #53: 60S ribosomal protein L9-A
+Macromolecule #54: 60S ribosomal protein L36-A
+Macromolecule #55: 60S ribosomal protein L10
+Macromolecule #56: 60S ribosomal protein L11-A
+Macromolecule #57: 60S ribosomal protein L37-A
+Macromolecule #58: 60S ribosomal protein L38
+Macromolecule #59: 60S ribosomal protein L39
+Macromolecule #60: 60S ribosomal protein L13-A
+Macromolecule #61: Ubiquitin-60S ribosomal protein L40
+Macromolecule #62: 60S ribosomal protein L14-A
+Macromolecule #63: 60S ribosomal protein L15-A
+Macromolecule #64: 60S ribosomal protein L42-B
+Macromolecule #65: 60S ribosomal protein L43-B
+Macromolecule #66: 60S ribosomal protein L17-A
+Macromolecule #67: 60S ribosomal protein L18-A
+Macromolecule #68: 60S ribosomal protein L20-A
+Macromolecule #69: 60S ribosomal protein L22-A
+Macromolecule #70: 60S ribosomal protein L23-A
+Macromolecule #71: 60S ribosomal protein L27-A
+Macromolecule #72: 60S ribosomal protein L16-A
+Macromolecule #73: 60S ribosomal protein L41-B
+Macromolecule #74: 60S ribosomal protein L19-A
+Macromolecule #75: 60S ribosomal protein L25
+Macromolecule #76: 60S ribosomal protein L26-A
+Macromolecule #77: 60S ribosomal protein L21-A
+Macromolecule #78: 60S ribosomal protein L6-A
+Macromolecule #79: 60S ribosomal protein L24-A
+Macromolecule #80: Protein HBS1
+Macromolecule #34: 18S ribosomal RNA
+Macromolecule #36: 25S ribosomal RNA
+Macromolecule #37: 5S ribosomal RNA
+Macromolecule #38: 5.8S ribosomal RNA
+Macromolecule #81: nonstop mRNA
+Macromolecule #82: yeast Phe-tRNA-Phe
+Macromolecule #83: ZINC ION
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #86: N-acetyl-L-phenylalanine
+Macromolecule #87: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-25 / Number real images: 4797 / Average exposure time: 5.0 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 80645 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-5m1j: |