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Yorodumi- EMDB-7836: Mammalian 80S ribosome with a double translocated CrPV-IRES, P-si... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7836 | |||||||||
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Title | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1. | |||||||||
Map data | post processed map with Bfactor -30 and low pass filtered to 7A with Chimera | |||||||||
Sample |
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Function / homology | Function and homology information Synthesis of diphthamide-EEF2 / ribosomal subunit / aggresome / 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 ...Synthesis of diphthamide-EEF2 / ribosomal subunit / aggresome / 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 / translational elongation / mammalian oogenesis stage / G1 to G0 transition / retinal ganglion cell axon guidance / Uptake and function of diphtheria toxin / activation-induced cell death of T cells / Peptide chain elongation / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / Protein methylation / hematopoietic progenitor cell differentiation / translation elongation factor activity / cellular response to actinomycin D / cytosolic ribosome / rough endoplasmic reticulum / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / 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 / regulation of translation / small ribosomal subunit / cell body / large ribosomal subunit rRNA binding / 5S rRNA binding / T cell differentiation in thymus / cytosolic small ribosomal subunit / perikaryon / secretory granule lumen / killing of cells of another organism / ficolin-1-rich granule lumen / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / tRNA binding / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / cadherin binding / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle 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_7836.map.gz | 184 MB | EMDB map data format | |
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Header (meta data) | emd-7836-v30.xml emd-7836.xml | 96.2 KB 96.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7836_fsc.xml | 16.6 KB | Display | FSC data file |
Images | emd_7836.png | 187 KB | ||
Masks | emd_7836_msk_1.map | 244.1 MB | Mask map | |
Others | emd_7836_additional.map.gz emd_7836_half_map_1.map.gz emd_7836_half_map_2.map.gz | 193.5 MB 194.7 MB 194 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7836 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7836 | HTTPS FTP |
-Validation report
Summary document | emd_7836_validation.pdf.gz | 840.4 KB | Display | EMDB validaton report |
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Full document | emd_7836_full_validation.pdf.gz | 839.9 KB | Display | |
Data in XML | emd_7836_validation.xml.gz | 22 KB | Display | |
Data in CIF | emd_7836_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7836 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7836 | HTTPS FTP |
-Related structure data
Related structure data | 6d9jMC 7834C 6d90C 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_7836.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 Bfactor -30 and low pass filtered to 7A with Chimera | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_7836_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_7836_additional.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_7836_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_7836_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mammalian 80S ribosome in complex with translocated CrPV IRES, P-...
+Supramolecule #1: Mammalian 80S ribosome in complex with translocated CrPV IRES, P-...
+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: eL18
+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 #50: uS2
+Macromolecule #51: eS1
+Macromolecule #52: uS5
+Macromolecule #53: uS3
+Macromolecule #54: eS4
+Macromolecule #55: uS7
+Macromolecule #56: eS6
+Macromolecule #57: eS7
+Macromolecule #58: eS8
+Macromolecule #59: uS4
+Macromolecule #60: eS10
+Macromolecule #61: uS17
+Macromolecule #62: eS12
+Macromolecule #63: uS15
+Macromolecule #64: uS11
+Macromolecule #65: uS19
+Macromolecule #66: uS9
+Macromolecule #67: eS17
+Macromolecule #68: uS13
+Macromolecule #69: eS19
+Macromolecule #70: uS10
+Macromolecule #71: eS21
+Macromolecule #72: uS8
+Macromolecule #73: uS12
+Macromolecule #74: eS24
+Macromolecule #75: eS25
+Macromolecule #76: eS26
+Macromolecule #77: eS27
+Macromolecule #78: eS28
+Macromolecule #79: eS29
+Macromolecule #80: eS30
+Macromolecule #81: eS31
+Macromolecule #82: RACK1
+Macromolecule #84: eEF2
+Macromolecule #45: 28S rRNA
+Macromolecule #46: 5S rRNA
+Macromolecule #47: 5.8S rRNA
+Macromolecule #49: 18S rRNA
+Macromolecule #83: P-site tRNA
+Macromolecule #85: CrPV IRES
+Macromolecule #86: ZINC ION
+Macromolecule #87: MAGNESIUM ION
-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 |