+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42525 | |||||||||
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Title | Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribosome assembly / translation / RIBOSOME | |||||||||
Function / homology | Function and homology information positive regulation of translational termination / positive regulation of translational elongation / ribosomal subunit / 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 / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...positive regulation of translational termination / positive regulation of translational elongation / ribosomal subunit / 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 / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / 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 / 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 / ribosomal large subunit export from nucleus / 90S preribosome / 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) / regulation of translational fidelity / protein-RNA complex assembly / translation elongation factor activity / ribosomal subunit export from nucleus / translation regulator 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) / maturation of LSU-rRNA / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / rescue of stalled ribosome / 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 / positive regulation of apoptotic signaling pathway / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / small ribosomal subunit / 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 / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
Authors | Yelland JN / Taylor DW / Johnson AW | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: The Ribosome Assembly Factor Reh1 is Released from the Polypeptide Exit Tunnel in the Pioneer Round of Translation Authors: Musalgaonkar S / Yelland JN / Chitale R / Rao S / Ozadam H / Cenik C / Taylor DW / Johnson AW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42525.map.gz | 900.1 MB | EMDB map data format | |
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Header (meta data) | emd-42525-v30.xml emd-42525.xml | 101 KB 101 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42525_fsc.xml | 21.5 KB | Display | FSC data file |
Images | emd_42525.png | 52.1 KB | ||
Filedesc metadata | emd-42525.cif.gz | 18.7 KB | ||
Others | emd_42525_half_map_1.map.gz emd_42525_half_map_2.map.gz | 963.2 MB 963.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42525 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42525 | HTTPS FTP |
-Validation report
Summary document | emd_42525_validation.pdf.gz | 1.4 MB | Display | EMDB validaton report |
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Full document | emd_42525_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | emd_42525_validation.xml.gz | 31 KB | Display | |
Data in CIF | emd_42525_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42525 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42525 | HTTPS FTP |
-Related structure data
Related structure data | 8ut0MC 8utiC 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_42525.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_42525_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42525_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA
+Supramolecule #1: Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA
+Macromolecule #1: 18S rRNA
+Macromolecule #35: 25S rRNA
+Macromolecule #36: 5S rRNA
+Macromolecule #37: 5.8S rRNA
+Macromolecule #81: A site tRNA
+Macromolecule #82: P site initiator tRNA
+Macromolecule #83: Messenger RNA (5'-R(P*AP*AP*UP*AP*UP*GP*AP*AP*AP*A)-3')
+Macromolecule #2: 40S ribosomal protein S0-A
+Macromolecule #3: 40S ribosomal protein S1-A
+Macromolecule #4: 40S ribosomal protein S15
+Macromolecule #5: 40S ribosomal protein S2
+Macromolecule #6: 40S ribosomal protein S3
+Macromolecule #7: 40S ribosomal protein S4-A
+Macromolecule #8: 40S ribosomal protein S5
+Macromolecule #9: 40S ribosomal protein S6-A
+Macromolecule #10: 40S ribosomal protein S7-A
+Macromolecule #11: 40S ribosomal protein S8-A
+Macromolecule #12: 40S ribosomal protein S9-A
+Macromolecule #13: 40S ribosomal protein S10-A
+Macromolecule #14: 40S ribosomal protein S11-A
+Macromolecule #15: 40S ribosomal protein S12
+Macromolecule #16: 40S ribosomal protein S13
+Macromolecule #17: 40S ribosomal protein S14-B
+Macromolecule #18: 40S ribosomal protein S16-A
+Macromolecule #19: 40S ribosomal protein S17-B
+Macromolecule #20: 40S ribosomal protein S18-A
+Macromolecule #21: 40S ribosomal protein S19-A
+Macromolecule #22: 40S ribosomal protein S20
+Macromolecule #23: 40S ribosomal protein S21-A
+Macromolecule #24: 40S ribosomal protein S22-A
+Macromolecule #25: 40S ribosomal protein S23-A
+Macromolecule #26: 40S ribosomal protein S24-A
+Macromolecule #27: 40S ribosomal protein S26-B
+Macromolecule #28: 40S ribosomal protein S27-A
+Macromolecule #29: 40S ribosomal protein S29-A
+Macromolecule #30: 40S ribosomal protein S30-A
+Macromolecule #31: 40S ribosomal protein S31
+Macromolecule #32: 40S ribosomal protein ASC1
+Macromolecule #33: 40S ribosomal protein S28-A
+Macromolecule #34: 40S ribosomal protein S25-A
+Macromolecule #38: 60S ribosomal protein L2-A
+Macromolecule #39: 60S ribosomal protein L3
+Macromolecule #40: 60S ribosomal protein L4-A
+Macromolecule #41: 60S ribosomal protein L5
+Macromolecule #42: 60S ribosomal protein L6-B
+Macromolecule #43: 60S ribosomal protein L7-A
+Macromolecule #44: 60S ribosomal protein L8-A
+Macromolecule #45: 60S ribosomal protein L9-A
+Macromolecule #46: 60S ribosomal protein L10
+Macromolecule #47: 60S ribosomal protein L11-B
+Macromolecule #48: 60S ribosomal protein L13-A
+Macromolecule #49: 60S ribosomal protein L14-A
+Macromolecule #50: 60S ribosomal protein L15-A
+Macromolecule #51: 60S ribosomal protein L16-A
+Macromolecule #52: 60S ribosomal protein L17-A
+Macromolecule #53: 60S ribosomal protein L18-A
+Macromolecule #54: 60S ribosomal protein L19-A
+Macromolecule #55: 60S ribosomal protein L20-A
+Macromolecule #56: 60S ribosomal protein L21-A
+Macromolecule #57: 60S ribosomal protein L22-A
+Macromolecule #58: 60S ribosomal protein L23-A
+Macromolecule #59: 60S ribosomal protein L24-A
+Macromolecule #60: 60S ribosomal protein L25
+Macromolecule #61: 60S ribosomal protein L26-A
+Macromolecule #62: 60S ribosomal protein L27-A
+Macromolecule #63: 60S ribosomal protein L28
+Macromolecule #64: 60S ribosomal protein L29
+Macromolecule #65: 60S ribosomal protein L30
+Macromolecule #66: 60S ribosomal protein L31-A
+Macromolecule #67: 60S ribosomal protein L32
+Macromolecule #68: 60S ribosomal protein L33-A
+Macromolecule #69: 60S ribosomal protein L34-A
+Macromolecule #70: 60S ribosomal protein L35-A
+Macromolecule #71: 60S ribosomal protein L36-A
+Macromolecule #72: 60S ribosomal protein L37-A
+Macromolecule #73: 60S ribosomal protein L38
+Macromolecule #74: 60S ribosomal protein L39
+Macromolecule #75: 60S ribosomal protein L40-A
+Macromolecule #76: 60S ribosomal protein L41-A
+Macromolecule #77: 60S ribosomal protein L42-A
+Macromolecule #78: 60S ribosomal protein L43-A
+Macromolecule #79: Translation factor eIF5A
+Macromolecule #80: Cytoplasmic 60S subunit biogenesis factor REH1 (N-terminal 3xFLAG tag)
+Macromolecule #84: 60S ribosomal protein L1
+Macromolecule #85: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
-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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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 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: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |