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Yorodumi- EMDB-22196: Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidati... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22196 | |||||||||
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Title | Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress | |||||||||
Map data | ||||||||||
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Function / homology | Function and homology information negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition ...negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / 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) / 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 / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G-protein alpha-subunit binding / positive regulation of protein kinase activity / regulation of translational fidelity / protein-RNA complex assembly / translation regulator activity / 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) / cellular response to amino acid starvation / rescue of stalled ribosome / 90S preribosome / 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 / maturation of SSU-rRNA / macroautophagy / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / ribosomal large subunit assembly / 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 / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Zhou Y / Bartesaghi A / Silva GM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress. Authors: Ye Zhou / Panagiotis L Kastritis / Shannon E Dougherty / Jonathan Bouvette / Allen L Hsu / Laura Burbaum / Shyamal Mosalaganti / Stefan Pfeffer / Wim J H Hagen / Friedrich Förster / Mario J ...Authors: Ye Zhou / Panagiotis L Kastritis / Shannon E Dougherty / Jonathan Bouvette / Allen L Hsu / Laura Burbaum / Shyamal Mosalaganti / Stefan Pfeffer / Wim J H Hagen / Friedrich Förster / Mario J Borgnia / Christine Vogel / Martin Beck / Alberto Bartesaghi / Gustavo M Silva / Abstract: Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational ...Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational modification that regulates protein synthesis during cellular response to oxidative stress. K63 ubiquitin, a type of ubiquitin chain that functions independently of the proteasome, modifies several sites at the surface of the ribosome, however, we lack a molecular understanding on how this modification affects ribosome structure and function. Using cryoelectron microscopy (cryo-EM), we resolved the first three-dimensional (3D) structures of K63 ubiquitinated ribosomes from oxidatively stressed yeast cells at 3.5-3.2 Å resolution. We found that K63 ubiquitinated ribosomes are also present in a polysome arrangement, similar to that observed in yeast polysomes, which we determined using cryoelectron tomography (cryo-ET). We further showed that K63 ubiquitinated ribosomes are captured uniquely at the rotated pretranslocation stage of translation elongation. In contrast, cryo-EM structures of ribosomes from mutant cells lacking K63 ubiquitin resolved at 4.4-2.7 Å showed 80S ribosomes represented in multiple states of translation, suggesting that K63 ubiquitin regulates protein synthesis at a selective stage of elongation. Among the observed structural changes, ubiquitin mediates the destabilization of proteins in the 60S P-stalk and in the 40S beak, two binding regions of the eukaryotic elongation factor eEF2. These changes would impact eEF2 function, thus, inhibiting translocation. Our findings help uncover the molecular effects of K63 ubiquitination on ribosomes, providing a model of translation control during oxidative stress, which supports elongation halt at pretranslocation. | |||||||||
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_22196.map.gz | 317.9 MB | EMDB map data format | |
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Header (meta data) | emd-22196-v30.xml emd-22196.xml | 97.3 KB 97.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22196_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_22196.png | 45.9 KB | ||
Masks | emd_22196_msk_1.map | 512 MB | Mask map | |
Others | emd_22196_half_map_1.map.gz emd_22196_half_map_2.map.gz | 410.6 MB 410.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22196 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22196 | HTTPS FTP |
-Validation report
Summary document | emd_22196_validation.pdf.gz | 894.9 KB | Display | EMDB validaton report |
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Full document | emd_22196_full_validation.pdf.gz | 894.5 KB | Display | |
Data in XML | emd_22196_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | emd_22196_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22196 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22196 | HTTPS FTP |
-Related structure data
Related structure data | 6xiqMC 6xirC C: citing same article (ref.) M: atomic model generated by this map |
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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_22196.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.066 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22196_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_22196_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_22196_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : K63 ubiquitinated Ribosome
+Supramolecule #1: K63 ubiquitinated Ribosome
+Macromolecule #1: 60S ribosomal protein L2-A
+Macromolecule #2: RPL3 isoform 1
+Macromolecule #3: RPL4A isoform 1
+Macromolecule #4: RPL5 isoform 1
+Macromolecule #5: 60S ribosomal protein L6-A
+Macromolecule #6: 60S ribosomal protein L7-A
+Macromolecule #7: RPL8A isoform 1
+Macromolecule #8: RPL9A isoform 1
+Macromolecule #9: RPL10 isoform 1
+Macromolecule #10: RPL11B isoform 1
+Macromolecule #11: 60S ribosomal protein L13-A
+Macromolecule #12: 60S ribosomal protein L14-A
+Macromolecule #13: 60S ribosomal protein L15-A
+Macromolecule #14: 60S ribosomal protein L16-A
+Macromolecule #15: 60S ribosomal protein L17-A
+Macromolecule #16: 60S ribosomal protein L18-A
+Macromolecule #17: 60S ribosomal protein L19-A
+Macromolecule #18: 60S ribosomal protein L20-A
+Macromolecule #19: 60S ribosomal protein L21-A
+Macromolecule #20: 60S ribosomal protein L22-A
+Macromolecule #21: 60S ribosomal protein L23-A
+Macromolecule #22: RPL24A isoform 1
+Macromolecule #23: 60S ribosomal protein L25
+Macromolecule #24: 60S ribosomal protein L26-A
+Macromolecule #25: 60S ribosomal protein L27-A
+Macromolecule #26: 40S ribosomal protein S10-A
+Macromolecule #27: 40S ribosomal protein S11-A
+Macromolecule #31: RPP0 isoform 1
+Macromolecule #32: RPL12A isoform 1
+Macromolecule #33: 60S ribosomal protein L28
+Macromolecule #34: RPL29 isoform 1
+Macromolecule #35: 60S ribosomal protein L30
+Macromolecule #36: 60S ribosomal protein L31-A
+Macromolecule #37: RPL32 isoform 1
+Macromolecule #38: 60S ribosomal protein L33-A
+Macromolecule #39: 60S ribosomal protein L34-A
+Macromolecule #40: 60S ribosomal protein L35-A
+Macromolecule #41: 60S ribosomal protein L36-A
+Macromolecule #42: 60S ribosomal protein L37-A
+Macromolecule #43: RPL38 isoform 1
+Macromolecule #44: 60S ribosomal protein L39
+Macromolecule #45: 60S ribosomal protein L40
+Macromolecule #46: RPL41A isoform 1
+Macromolecule #47: 60S ribosomal protein L42-A
+Macromolecule #48: 60S ribosomal protein L43-A
+Macromolecule #50: 40S ribosomal protein S0-A
+Macromolecule #51: RPS1A isoform 1
+Macromolecule #52: RPS2 isoform 1
+Macromolecule #53: RPS3 isoform 1
+Macromolecule #54: 40S ribosomal protein S4-A
+Macromolecule #55: Rps5p
+Macromolecule #56: 40S ribosomal protein S6-A
+Macromolecule #57: 40S ribosomal protein S7-A
+Macromolecule #58: RPS8A isoform 1
+Macromolecule #59: 40S ribosomal protein S9-A
+Macromolecule #60: 40S ribosomal protein S13
+Macromolecule #61: 40S ribosomal protein S14-B
+Macromolecule #62: RPS15 isoform 1
+Macromolecule #63: 40S ribosomal protein S16-A
+Macromolecule #64: 40S ribosomal protein S17-B
+Macromolecule #65: 40S ribosomal protein S18-A
+Macromolecule #66: 40S ribosomal protein S19-A
+Macromolecule #67: RPS20 isoform 1
+Macromolecule #68: 40S ribosomal protein S21-A
+Macromolecule #69: RPS22A isoform 1
+Macromolecule #70: 40S ribosomal protein S23-A
+Macromolecule #71: 40S ribosomal protein S24-A
+Macromolecule #72: RPS25A isoform 1
+Macromolecule #73: RPS26B isoform 1
+Macromolecule #74: 40S ribosomal protein S27-A
+Macromolecule #75: RPS28A isoform 1
+Macromolecule #76: RPS29A isoform 1
+Macromolecule #77: 40S ribosomal protein S30-A
+Macromolecule #78: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #81: RPL1A isoform 1
+Macromolecule #28: 35S ribosomal RNA
+Macromolecule #29: 5S ribosomal RNA
+Macromolecule #30: 5.8S ribosomal RNA
+Macromolecule #49: 18S ribosomal RNA
+Macromolecule #79: Transfer RNA
+Macromolecule #80: mRNA
+Macromolecule #82: ZINC ION
-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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Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3138 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |