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Yorodumi- EMDB-7834: Mammalian 80S ribosome with a double translocated CrPV-IRES, P-si... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7834 | |||||||||
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Title | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1. | |||||||||
Map data | post-processed map with B-factor -30 and low pass filter to 4.8A | |||||||||
Sample |
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Function / homology | Function and homology information translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / ribosomal subunit / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...translation termination factor activity / translation release factor complex / cytoplasmic translational termination / translation release factor activity / regulation of translational termination / ribosomal subunit / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / aminoacyl-tRNA hydrolase activity / laminin receptor activity / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / mammalian oogenesis stage / G1 to G0 transition / retinal ganglion cell axon guidance / activation-induced cell death of T cells / Protein hydroxylation / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / translational termination / rough endoplasmic reticulum / laminin binding / 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) / gastrulation / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / negative regulation of ubiquitin-dependent protein catabolic process / 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 / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosomal small subunit assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / retina development in camera-type eye / glucose homeostasis / virus receptor activity / regulation of translation / heparin binding / small ribosomal subunit / cell body / large ribosomal subunit rRNA binding / 5S rRNA binding / T cell differentiation in thymus / cytosolic small ribosomal subunit / perikaryon / killing of cells of another organism / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / tRNA binding / postsynaptic density Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) / Homo sapiens (human) / Escherichia coli (E. coli) / Cricket paralysis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Pisareva VP / Pisarev AV / Fernandez IS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2018 Title: Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES. Authors: Vera P Pisareva / Andrey V Pisarev / Israel S Fernández / Abstract: Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its ...Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its structural genes in the late stage of infection. Ribosome hijacking is achieved by a sophisticated use of molecular mimicry to tRNA and mRNA, employed to manipulate intrinsically dynamic components of the ribosome. Binding and translocation through the ribosome is required for this IRES to initiate translation. We report two structures, solved by single particle electron cryo-microscopy (cryoEM), of a double translocated CrPV-IRES with aminoacyl-tRNA in the peptidyl site (P site) of the ribosome. CrPV-IRES adopts a previously unseen conformation, mimicking the acceptor stem of a canonical E site tRNA. The structures suggest a mechanism for the positioning of the first aminoacyl-tRNA shared with the distantly related Hepatitis C Virus IRES. | |||||||||
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_7834.map.gz | 37.5 MB | EMDB map data format | |
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Header (meta data) | emd-7834-v30.xml emd-7834.xml | 93.4 KB 93.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7834_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_7834.png | 173.6 KB | ||
Masks | emd_7834_msk_1.map | 244.1 MB | Mask map | |
Others | emd_7834_additional_1.map.gz emd_7834_additional_2.map.gz | 193.6 MB 40.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7834 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7834 | HTTPS FTP |
-Validation report
Summary document | emd_7834_validation.pdf.gz | 450.5 KB | Display | EMDB validaton report |
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Full document | emd_7834_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | emd_7834_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_7834_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7834 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7834 | HTTPS FTP |
-Related structure data
Related structure data | 6d90MC 7836C 6d9jC 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_7834.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | post-processed map with B-factor -30 and low pass filter to 4.8A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 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_7834_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_7834_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: post-processed map using autoBfactor option in Relion
File | emd_7834_additional_2.map | ||||||||||||
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Annotation | post-processed map using autoBfactor option in Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mammalian 80S ribosome in complex with a double translocated CrPV...
+Supramolecule #1: Mammalian 80S ribosome in complex with a double translocated CrPV...
+Macromolecule #1: uL2
+Macromolecule #2: uL3
+Macromolecule #3: uL4
+Macromolecule #4: uL18
+Macromolecule #5: eL6
+Macromolecule #6: uL30
+Macromolecule #7: eL8
+Macromolecule #8: uL6
+Macromolecule #9: uL16
+Macromolecule #10: uL11
+Macromolecule #11: eL13
+Macromolecule #12: eL14
+Macromolecule #13: eL15
+Macromolecule #14: uL13
+Macromolecule #15: uL22
+Macromolecule #16: rL18
+Macromolecule #17: eL19
+Macromolecule #18: eL20
+Macromolecule #19: eL21
+Macromolecule #20: eL22
+Macromolecule #21: uL14
+Macromolecule #22: eL24
+Macromolecule #23: eL23
+Macromolecule #24: uL24
+Macromolecule #25: eL27
+Macromolecule #26: uL15
+Macromolecule #27: eL29
+Macromolecule #28: eL30
+Macromolecule #29: eL31
+Macromolecule #30: eL32
+Macromolecule #31: eL33
+Macromolecule #32: eL34
+Macromolecule #33: eL35
+Macromolecule #34: eL36
+Macromolecule #35: eL37
+Macromolecule #36: eL38
+Macromolecule #37: eL39
+Macromolecule #38: eL40
+Macromolecule #39: eL41
+Macromolecule #40: eL42
+Macromolecule #41: eL43
+Macromolecule #42: eL28
+Macromolecule #43: uL10
+Macromolecule #44: uL11
+Macromolecule #48: uL1
+Macromolecule #51: uS2
+Macromolecule #52: eS1
+Macromolecule #53: uS5
+Macromolecule #54: uS3
+Macromolecule #55: eS4
+Macromolecule #56: uS7
+Macromolecule #57: eS6
+Macromolecule #58: eS7
+Macromolecule #59: eS8
+Macromolecule #60: uS4
+Macromolecule #61: eS10
+Macromolecule #62: uS17
+Macromolecule #63: eS12
+Macromolecule #64: uS15
+Macromolecule #65: uS11
+Macromolecule #66: uS19
+Macromolecule #67: uS9
+Macromolecule #68: eS17
+Macromolecule #69: uS13
+Macromolecule #70: eS19
+Macromolecule #71: uS10
+Macromolecule #72: eS21
+Macromolecule #73: uS8
+Macromolecule #74: uS12
+Macromolecule #75: eS24
+Macromolecule #76: eS25
+Macromolecule #77: eS26
+Macromolecule #78: eS27
+Macromolecule #79: eS28
+Macromolecule #80: eS29
+Macromolecule #81: eS30
+Macromolecule #82: eS31
+Macromolecule #83: RACK1
+Macromolecule #84: eRF1
+Macromolecule #45: 28S rRNA
+Macromolecule #46: 5S rRNA
+Macromolecule #47: 5.8S rRNA
+Macromolecule #49: 18S rRNA
+Macromolecule #50: P-tRNA
+Macromolecule #85: CrPV-IRES
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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 K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |