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Yorodumi- PDB-6d9j: Mammalian 80S ribosome with a double translocated CrPV-IRES, P-si... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d9j | ||||||
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Title | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1. | ||||||
Components |
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Keywords | RIBOSOME / mammalian / CrPV IRES | ||||||
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 | Homo sapiens (human) Oryctolagus cuniculus (rabbit) Escherichia coli (E. coli) Cricket paralysis virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Pisareva, V.P. / Pisarev, A.V. / Fernandez, I.S. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6d9j.cif.gz | 5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6d9j.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6d9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6d9j_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6d9j_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6d9j_validation.xml.gz | 368.7 KB | Display | |
Data in CIF | 6d9j_validation.cif.gz | 639.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/6d9j ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d9j | HTTPS FTP |
-Related structure data
Related structure data | 7836MC 7834C 6d90C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 78 types, 78 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-Protein/peptide , 1 types, 1 molecules n
#39: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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-RNA chain , 6 types, 6 molecules 578234
#45: RNA chain | Mass: 1164731.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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#46: RNA chain | Mass: 38385.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: REF: 1304938343 |
#47: RNA chain | Mass: 48545.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#49: RNA chain | Mass: 547733.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#83: RNA chain | Mass: 28094.645 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription with T7 RNA polymerase Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1370526512 |
#85: RNA chain | Mass: 60789.762 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription with T7 RNA polymerase Source: (synth.) Cricket paralysis virus / References: GenBank: 8895506 |
-Non-polymers , 2 types, 6 molecules
#86: Chemical | ChemComp-ZN / #87: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mammalian 80S ribosome in complex with translocated CrPV IRES, P-site tRNA and eEF2 Type: RIBOSOME Details: Mammalian 80S ribosome in complex with translocated CrPV IRES, P-site tRNA and eRF1 Entity ID: #1-#85 / Source: NATURAL |
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Molecular weight | Value: 5 MDa / Experimental value: NO |
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75654 / Symmetry type: POINT |