+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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Function / homology | Function and homology information Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / mRNA decay by 3' to 5' exoribonuclease / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / 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 ...Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / mRNA decay by 3' to 5' exoribonuclease / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / 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 / 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 / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / 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 / RNA endonuclease activity / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / ribosome assembly / small-subunit processome / protein kinase C binding / positive regulation of translation / meiotic cell cycle / maintenance of translational fidelity / macroautophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / protein tag activity / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / G protein-coupled receptor signaling pathway / cell division / negative regulation of gene expression / response to antibiotic / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / nucleolus / mitochondrion / RNA binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Hilal T / Yamamoto H / Loerke J / Buerger J / Mielke T / Spahn CMT | |||||||||
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 | 91.5 KB 91.5 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 | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4140 ftp://ftp.pdbj.org/pub/emdb/structures/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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 80645 |
Sample stage | Cooling holder cryogen: NITROGEN |
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 |
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: |