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Yorodumi- EMDB-21859: CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21859 | |||||||||
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Title | CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP | |||||||||
Map data | post-processed map, masked | |||||||||
Sample |
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Keywords | yeast / ribosome / initiation / eIF5B / GDP / Met-tRNAiMet | |||||||||
Function / homology | Function and homology information : / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / protein-synthesizing GTPase / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / eukaryotic 48S preinitiation complex / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / positive regulation of translational fidelity ...: / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / protein-synthesizing GTPase / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / eukaryotic 48S preinitiation complex / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / positive regulation of translational fidelity / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / regulation of translational initiation / nonfunctional rRNA decay / 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 / 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 / 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 / regulation of amino acid metabolic process / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / Ub-specific processing proteases / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / 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 / translation initiation factor binding / translation initiation factor activity / maturation of LSU-rRNA / cellular response to amino acid starvation / rescue of stalled ribosome / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cytosolic ribosome assembly / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosome biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / 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 / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / nucleolus / mitochondrion / RNA binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Wang J | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex. Authors: Jinfan Wang / Jing Wang / Byung-Sik Shin / Joo-Ran Kim / Thomas E Dever / Joseph D Puglisi / Israel S Fernández / Abstract: Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the ...Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNA on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNA immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit. | |||||||||
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_21859.map.gz | 19.9 MB | EMDB map data format | |
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Header (meta data) | emd-21859-v30.xml emd-21859.xml | 104.5 KB 104.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21859_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_21859.png | 117.2 KB | ||
Masks | emd_21859_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-21859.cif.gz | 19.1 KB | ||
Others | emd_21859_additional_1.map.gz emd_21859_additional_2.map.gz emd_21859_half_map_1.map.gz emd_21859_half_map_2.map.gz | 85.4 MB 18.7 MB 85.6 MB 85.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21859 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21859 | HTTPS FTP |
-Validation report
Summary document | emd_21859_validation.pdf.gz | 1000 KB | Display | EMDB validaton report |
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Full document | emd_21859_full_validation.pdf.gz | 999.6 KB | Display | |
Data in XML | emd_21859_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_21859_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21859 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21859 | HTTPS FTP |
-Related structure data
Related structure data | 6wooMC 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_21859.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | post-processed map, masked | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.416 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_21859_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_21859_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: post-processed map, with Bfactor -50 and low-pass filtered to 3.3A
File | emd_21859_additional_2.map | ||||||||||||
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Annotation | post-processed map, with Bfactor -50 and low-pass filtered to 3.3A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-1
File | emd_21859_half_map_1.map | ||||||||||||
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Annotation | half-1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 2
File | emd_21859_half_map_2.map | ||||||||||||
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Annotation | half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 80S ribosome with eIF5B, Met-tRNAiMet, mRNA, and GDP
+Supramolecule #1: 80S ribosome with eIF5B, Met-tRNAiMet, mRNA, and GDP
+Macromolecule #1: 25S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal rRNA
+Macromolecule #81: 18S ribosomal RNA
+Macromolecule #83: Met-tRNA-iMet
+Macromolecule #84: mRNA
+Macromolecule #4: uL2
+Macromolecule #5: uL3
+Macromolecule #6: uL4
+Macromolecule #7: uL18
+Macromolecule #8: eL6
+Macromolecule #9: uL30
+Macromolecule #10: eL8
+Macromolecule #11: uL6
+Macromolecule #12: uL16
+Macromolecule #13: uL5
+Macromolecule #14: eL13
+Macromolecule #15: eL14
+Macromolecule #16: eL15
+Macromolecule #17: uL13
+Macromolecule #18: uL22
+Macromolecule #19: eL18
+Macromolecule #20: eL19
+Macromolecule #21: eL20
+Macromolecule #22: eL21
+Macromolecule #23: eL22
+Macromolecule #24: uL14
+Macromolecule #25: eL24
+Macromolecule #26: uL23
+Macromolecule #27: uL24
+Macromolecule #28: eL27
+Macromolecule #29: uL15
+Macromolecule #30: eL29
+Macromolecule #31: eL30
+Macromolecule #32: eL31
+Macromolecule #33: eL32
+Macromolecule #34: eL33
+Macromolecule #35: eL34
+Macromolecule #36: uL29
+Macromolecule #37: eL36
+Macromolecule #38: eL37
+Macromolecule #39: eL38
+Macromolecule #40: eL39
+Macromolecule #41: eL40
+Macromolecule #42: eL41
+Macromolecule #43: eL42
+Macromolecule #44: eL43
+Macromolecule #45: uL1
+Macromolecule #46: uL10
+Macromolecule #47: L10
+Macromolecule #48: uS2
+Macromolecule #49: eS1
+Macromolecule #50: uS5
+Macromolecule #51: uS3
+Macromolecule #52: eS4
+Macromolecule #53: uS7
+Macromolecule #54: eS6
+Macromolecule #55: eS7
+Macromolecule #56: eS8
+Macromolecule #57: uS4
+Macromolecule #58: eS10
+Macromolecule #59: uS17
+Macromolecule #60: eS12
+Macromolecule #61: uS15
+Macromolecule #62: uS11
+Macromolecule #63: uS19
+Macromolecule #64: uS19
+Macromolecule #65: eS17
+Macromolecule #66: uS13
+Macromolecule #67: eS19
+Macromolecule #68: uS10
+Macromolecule #69: eS21
+Macromolecule #70: uS8
+Macromolecule #71: uS12
+Macromolecule #72: eS24
+Macromolecule #73: eS25
+Macromolecule #74: eS26
+Macromolecule #75: eS27
+Macromolecule #76: eS28
+Macromolecule #77: uS14
+Macromolecule #78: eS30
+Macromolecule #79: eS31
+Macromolecule #80: RACK1
+Macromolecule #82: eIF5B
+Macromolecule #85: ZINC ION
+Macromolecule #86: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #87: N-carboxy-L-threonine
+Macromolecule #88: METHIONINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |