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Yorodumi- EMDB-16470: Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S com... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16470 | ||||||||||||||||||
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Title | Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S complex - body 1 | ||||||||||||||||||
Map data | Cryo-EM map of in vitro reconstituted Otu2-Ub-40S complex - body 1 | ||||||||||||||||||
Sample |
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Keywords | 40S / Ubiquitin / Deubiquitinating enzyme / Otu2 / Rps7 / RIBOSOME | ||||||||||||||||||
Function / homology | Function and homology information maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / ribosomal subunit export from nucleus / 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) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cysteine-type deubiquitinase activity / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | ||||||||||||||||||
Authors | Ikeuchi K / Buschauer R / Cheng J / Berninghausen O / Becker T / Beckmann R | ||||||||||||||||||
Funding support | Germany, Japan, 5 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Authors: Ken Ikeuchi / Nives Ivic / Robert Buschauer / Jingdong Cheng / Thomas Fröhlich / Yoshitaka Matsuo / Otto Berninghausen / Toshifumi Inada / Thomas Becker / Roland Beckmann / Abstract: In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its ...In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome recycling and initiation stages. Otu2 binds to several sites on the intersubunit surface of the 40S that are not occupied by any other 40S-binding factors. This binding mode explains the discrimination against 80S ribosomes via the largely helical N-terminal domain of Otu2 as well as the specificity for mono-ubiquitinated eS7 on 40S. Collectively, this study reveals mechanistic insights into the Otu2-driven deubiquitination steps for translational reset during ribosome recycling/(re)initiation. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16470.map.gz | 106.5 MB | EMDB map data format | |
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Header (meta data) | emd-16470-v30.xml emd-16470.xml | 36.8 KB 36.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16470_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_16470.png | 80 KB | ||
Filedesc metadata | emd-16470.cif.gz | 9.1 KB | ||
Others | emd_16470_half_map_1.map.gz emd_16470_half_map_2.map.gz | 122 MB 122 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16470 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16470 | HTTPS FTP |
-Validation report
Summary document | emd_16470_validation.pdf.gz | 903.1 KB | Display | EMDB validaton report |
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Full document | emd_16470_full_validation.pdf.gz | 902.7 KB | Display | |
Data in XML | emd_16470_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | emd_16470_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16470 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16470 | HTTPS FTP |
-Related structure data
Related structure data | 8c83MC 8cahC 8casC 8cbjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16470.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of in vitro reconstituted Otu2-Ub-40S complex - body 1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_16470_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_16470_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : in vitro reconstituted yeast 40S ribosome complex with deubiquiti...
+Supramolecule #1: in vitro reconstituted yeast 40S ribosome complex with deubiquiti...
+Supramolecule #2: OTU domain-containing protein 2; Ubiquitin
+Supramolecule #3: yeast 40S ribosome complex
+Macromolecule #1: OTU domain-containing protein 2
+Macromolecule #2: Ubiquitin
+Macromolecule #4: 40S ribosomal protein S0-A
+Macromolecule #5: 40S ribosomal protein S2
+Macromolecule #6: 40S ribosomal protein S4-A
+Macromolecule #7: 40S ribosomal protein S6-A
+Macromolecule #8: 40S ribosomal protein S7-A
+Macromolecule #9: 40S ribosomal protein S8-B
+Macromolecule #10: 40S ribosomal protein S9-A
+Macromolecule #11: 40S ribosomal protein S11-A
+Macromolecule #12: 40S ribosomal protein S13
+Macromolecule #13: 40S ribosomal protein S21-A
+Macromolecule #14: 40S ribosomal protein S22-A
+Macromolecule #15: 40S ribosomal protein S23-A
+Macromolecule #16: 40S ribosomal protein S24-A
+Macromolecule #17: 40S ribosomal protein S27-A
+Macromolecule #18: 40S ribosomal protein S30-A
+Macromolecule #3: 18S ribosomal RNA
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 46.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |