+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23934 | |||||||||
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Title | Stm1 bound vacant 80S structure isolated from cbf5-D95A | |||||||||
Map data | Composite map | |||||||||
Sample |
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Function / homology | Function and homology information triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / 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 ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / 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 / 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 / telomeric DNA binding / 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 / TOR signaling / 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 / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / translational termination / translation repressor activity / 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 / maturation of LSU-rRNA / telomere maintenance / 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 / 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 / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / mitochondrion / DNA binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Rai J / Zhao Y / Li H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Structure / Year: 2022 Title: CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations. Authors: Yu Zhao / Jay Rai / Hongguo Yu / Hong Li / Abstract: Pseudouridine, the most abundant form of RNA modification, is known to play important roles in ribosome function. Mutations in human DKC1, the pseudouridine synthase responsible for catalyzing the ...Pseudouridine, the most abundant form of RNA modification, is known to play important roles in ribosome function. Mutations in human DKC1, the pseudouridine synthase responsible for catalyzing the ribosome RNA modification, cause translation deficiencies and are associated with a complex cancer predisposition. The structural basis for how pseudouridine impacts ribosome function remains uncharacterized. Here, we characterized structures and conformations of a fully modified and a pseudouridine-free ribosome from Saccharomyces cerevisiae in the absence of ligands or when bound with translocation inhibitor cycloheximide by electron cryomicroscopy. In the modified ribosome, the rearranged N1 atom of pseudouridine is observed to stabilize key functional motifs by establishing predominately water-mediated close contacts with the phosphate backbone. The pseudouridine-free ribosome, however, is devoid of such interactions and displays conformations reflective of abnormal inter-subunit movements. The erroneous motions of the pseudouridine-free ribosome may explain its observed deficiencies in translation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_23934.map.gz | 261.9 MB | EMDB map data format | |
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Header (meta data) | emd-23934-v30.xml emd-23934.xml | 102.6 KB 102.6 KB | Display Display | EMDB header |
Images | emd_23934.png | 109.5 KB | ||
Others | emd_23934_additional_1.map.gz emd_23934_additional_2.map.gz emd_23934_additional_3.map.gz | 278.7 MB 258.2 MB 279.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23934 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23934 | HTTPS FTP |
-Validation report
Summary document | emd_23934_validation.pdf.gz | 516.5 KB | Display | EMDB validaton report |
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Full document | emd_23934_full_validation.pdf.gz | 516.1 KB | Display | |
Data in XML | emd_23934_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_23934_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23934 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23934 | HTTPS FTP |
-Related structure data
Related structure data | 7mpiMC 7mpjC 7n8bC 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_23934.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.074 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Focus refinement of 40S body-349,046 particles-3.03 Angstrom 2.99...
File | emd_23934_additional_1.map | ||||||||||||
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Annotation | Focus refinement of 40S body-349,046 particles-3.03 Angstrom 2.99 Angstrom | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focus refinement of 60S-404,065 particles -2.89 Angstrom
File | emd_23934_additional_2.map | ||||||||||||
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Annotation | Focus refinement of 60S-404,065 particles -2.89 Angstrom | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focus refinement of 40S head-349,046 particles-3.03 Angstrom
File | emd_23934_additional_3.map | ||||||||||||
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Annotation | Focus refinement of 40S head-349,046 particles-3.03 Angstrom | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : composite map of Stm1 bound vacant 80S structure isolated from cb...
+Supramolecule #1: composite map of Stm1 bound vacant 80S structure isolated from cb...
+Supramolecule #2: 40S-body of Stm1 bound vacant 80S structure isolated from cbf5-D95A
+Supramolecule #3: 40S-head of Stm1 bound vacant 80S structure isolated from cbf5-D95A
+Supramolecule #4: 60S subunit of Stm1 bound vacant 80S structure isolated from cbf5-D95A
+Macromolecule #1: 40S ribosomal protein S0-A
+Macromolecule #2: 40S ribosomal protein S1-A
+Macromolecule #3: 40S ribosomal protein S2
+Macromolecule #4: 40S ribosomal protein S3
+Macromolecule #5: 40S ribosomal protein S4-A
+Macromolecule #6: 40S ribosomal protein S5
+Macromolecule #7: 40S ribosomal protein S6-A
+Macromolecule #8: 40S ribosomal protein S7-A
+Macromolecule #9: 40S ribosomal protein S8-A
+Macromolecule #10: 40S ribosomal protein S9-A
+Macromolecule #11: 40S ribosomal protein S10-A
+Macromolecule #12: 40S ribosomal protein S11-A
+Macromolecule #13: 40S ribosomal protein S12
+Macromolecule #14: 40S ribosomal protein S13
+Macromolecule #15: 40S ribosomal protein S14-A
+Macromolecule #16: 40S ribosomal protein S15
+Macromolecule #17: 40S ribosomal protein S16-A
+Macromolecule #18: 40S ribosomal protein S17-A
+Macromolecule #19: 40S ribosomal protein S18-A
+Macromolecule #20: 40S ribosomal protein S19-A
+Macromolecule #21: 40S ribosomal protein S20
+Macromolecule #22: 40S ribosomal protein S21-A
+Macromolecule #23: 40S ribosomal protein S22-A
+Macromolecule #24: 40S ribosomal protein S23-A
+Macromolecule #25: 40S ribosomal protein S24-A
+Macromolecule #26: 40S ribosomal protein S25-A
+Macromolecule #27: 40S ribosomal protein S26-B
+Macromolecule #28: 40S ribosomal protein S27-A
+Macromolecule #29: 40S ribosomal protein S28-A
+Macromolecule #30: 40S ribosomal protein S29-A
+Macromolecule #31: 40S ribosomal protein S30-A
+Macromolecule #32: 40S ribosomal protein S31
+Macromolecule #33: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #34: Suppressor protein STM1
+Macromolecule #39: 60S ribosomal protein L2-A
+Macromolecule #40: 60S ribosomal protein L3
+Macromolecule #41: 60S ribosomal protein L4-A
+Macromolecule #42: 60S ribosomal protein L5
+Macromolecule #43: 60S ribosomal protein L6-A
+Macromolecule #44: 60S ribosomal protein L7-A
+Macromolecule #45: 60S ribosomal protein L8-A
+Macromolecule #46: 60S ribosomal protein L9-A
+Macromolecule #47: 60S ribosomal protein L10
+Macromolecule #48: 60S ribosomal protein L11-A
+Macromolecule #49: 60S ribosomal protein L13-A
+Macromolecule #50: 60S ribosomal protein L14-A
+Macromolecule #51: 60S ribosomal protein L15-A
+Macromolecule #52: 60S ribosomal protein L16-A
+Macromolecule #53: 60S ribosomal protein L17-A
+Macromolecule #54: 60S ribosomal protein L18-A
+Macromolecule #55: 60S ribosomal protein L19-A
+Macromolecule #56: 60S ribosomal protein L20-A
+Macromolecule #57: 60S ribosomal protein L21-A
+Macromolecule #58: 60S ribosomal protein L22-A
+Macromolecule #59: 60S ribosomal protein L23-A
+Macromolecule #60: 60S ribosomal protein L24-A
+Macromolecule #61: 60S ribosomal protein L25
+Macromolecule #62: 60S ribosomal protein L26-A
+Macromolecule #63: 60S ribosomal protein L27-A
+Macromolecule #64: 60S ribosomal protein L28
+Macromolecule #65: 60S ribosomal protein L29
+Macromolecule #66: 60S ribosomal protein L30
+Macromolecule #67: 60S ribosomal protein L31-A
+Macromolecule #68: 60S ribosomal protein L32
+Macromolecule #69: 60S ribosomal protein L33-A
+Macromolecule #70: 60S ribosomal protein L34-A
+Macromolecule #71: 60S ribosomal protein L35-A
+Macromolecule #72: 60S ribosomal protein L36-A
+Macromolecule #73: 60S ribosomal protein L37-A
+Macromolecule #74: 60S ribosomal protein L38
+Macromolecule #75: 60S ribosomal protein L39
+Macromolecule #76: 60S ribosomal protein L40-A
+Macromolecule #77: 60S ribosomal protein L41-A
+Macromolecule #78: 60S ribosomal protein L42-A
+Macromolecule #79: 60S ribosomal protein L43-A
+Macromolecule #35: 18S rRNA
+Macromolecule #36: 25S rRNA
+Macromolecule #37: 5s rRNA
+Macromolecule #38: 5.8 S rRNA
+Macromolecule #80: MAGNESIUM ION
+Macromolecule #81: 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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: OTHER / Number images used: 404065 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |