+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23935 | |||||||||
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Title | Stm1 bound vacant 80S structure isolated from wild-type | |||||||||
Map data | Composite map | |||||||||
Sample |
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Keywords | yeast / 80S complex / chemical modification / RIBOSOME | |||||||||
Function / homology | Function and homology information triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / 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 / RMTs methylate histone arginines ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / Platelet degranulation / regulation of translational initiation in response to stress / 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 / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / hexon binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / preribosome, small subunit precursor / 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 / response to cycloheximide / telomeric DNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / positive regulation of protein kinase activity / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / Ub-specific processing proteases / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / 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 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / viral capsid / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / negative regulation of apoptotic process / host cell nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Rai J / Zhao Y | |||||||||
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_23935.map.gz | 287 MB | EMDB map data format | |
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Header (meta data) | emd-23935-v30.xml emd-23935.xml | 109.7 KB 109.7 KB | Display Display | EMDB header |
Images | emd_23935.png | 147.7 KB | ||
Filedesc metadata | emd-23935.cif.gz | 18.2 KB | ||
Others | emd_23935_additional_1.map.gz emd_23935_additional_2.map.gz emd_23935_additional_3.map.gz | 288 MB 288.1 MB 287.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23935 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23935 | HTTPS FTP |
-Validation report
Summary document | emd_23935_validation.pdf.gz | 640.7 KB | Display | EMDB validaton report |
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Full document | emd_23935_full_validation.pdf.gz | 640.2 KB | Display | |
Data in XML | emd_23935_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_23935_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23935 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23935 | HTTPS FTP |
-Related structure data
Related structure data | 7mpjMC 7mpiC 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_23935.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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: 60S subunit-288240 particles-2.57 angstorm
File | emd_23935_additional_1.map | ||||||||||||
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Annotation | 60S subunit-288240 particles-2.57 angstorm | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 40S body-289345 particles-2.72 Angstrom
File | emd_23935_additional_2.map | ||||||||||||
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Annotation | 40S body-289345 particles-2.72 Angstrom | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 40S head-289345 particles-2.72 Angstrom
File | emd_23935_additional_3.map | ||||||||||||
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Annotation | 40S head-289345 particles-2.72 Angstrom | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Composite map
+Supramolecule #1: Composite map
+Supramolecule #2: 40S-body of Stm1 bound vacant 80S structure isolated from nop1-D243A.
+Supramolecule #3: 40S head of Stm1 bound vacant 80S structure isolated from nop1-D243A.
+Supramolecule #4: 60S subnit of Stm1 bound vacant 80S structure isolated from nop1-...
+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-A
+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: 5.8S 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
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: OTHER / Number images used: 289345 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |