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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 / 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 / Uptake and function of diphtheria toxin ...Synthesis of diphthamide-EEF2 / 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 / Uptake and function of diphtheria toxin / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / Peptide chain elongation / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / translational elongation / TOR signaling / 90S preribosome / T cell proliferation involved in immune response / translation elongation factor activity / erythrocyte development / hematopoietic progenitor cell differentiation / negative regulation of ubiquitin-dependent protein catabolic process / Protein methylation / translation regulator activity / cellular response to actinomycin D / ribosomal small subunit export from nucleus / 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 / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / 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 / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / ribosome biogenesis / ribosome binding / retina development in camera-type eye / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / secretory granule lumen / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / ficolin-1-rich granule lumen / cytoplasmic translation / cell differentiation / tRNA binding / postsynaptic density / protein stabilization / rRNA binding / mitochondrial inner membrane / ribosome / protein ubiquitination / structural constituent of ribosome / cadherin binding / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / cell division / DNA repair 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 |