- EMDB-7836: Mammalian 80S ribosome with a double translocated CrPV-IRES, P-si... -
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Basic information
Entry
Database: EMDB / ID: EMD-7836
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
Complex: Mammalian 80S ribosome in complex with translocated CrPV IRES, P-site tRNA and eEF2
Protein or peptide: x 79 types
RNA: x 6 types
Ligand: x 2 types
Keywords
ribosome / mammalian / CrPV IRES
Function / homology
Function and homology information
Synthesis of diphthamide-EEF2 / ribosomal subunit / aggresome / exit from mitosis / optic nerve development / retinal ganglion cell axon guidance / lncRNA binding / Uptake and function of diphtheria toxin / Peptide chain elongation / positive regulation of signal transduction by p53 class mediator ...Synthesis of diphthamide-EEF2 / ribosomal subunit / aggresome / exit from mitosis / optic nerve development / retinal ganglion cell axon guidance / lncRNA binding / Uptake and function of diphtheria toxin / Peptide chain elongation / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / translational elongation / phagocytic cup / 90S preribosome / translation elongation factor activity / hematopoietic progenitor cell differentiation / Protein methylation / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of translation / maturation of SSU-rRNA / small-subunit processome / spindle / mRNA 5'-UTR binding / antimicrobial humoral immune response mediated by antimicrobial peptide / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / regulation of translation / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / retina development in camera-type eye / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / defense response to Gram-negative bacterium / secretory granule lumen / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / killing of cells of another organism / perikaryon / cytosolic large ribosomal subunit / ficolin-1-rich granule lumen / cytoplasmic translation / cell differentiation / tRNA binding / mitochondrial inner membrane / postsynaptic density / rRNA binding / ribosome / structural constituent of ribosome / cadherin binding / translation / ribonucleoprotein complex / cell division / DNA repair / GTPase activity / mRNA binding / apoptotic process / synapse / centrosome / dendrite / Neutrophil degranulation / negative regulation of apoptotic process / protein kinase binding / GTP binding / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function
60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type ...60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ubiquitin-like protein FUBI / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Ribosomal L15/L27a, N-terminal / Elongation factor G C-terminus / Ribosomal protein L28e / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Ribosomal protein L23 / EF-G domain III/V-like / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / : / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L6e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / : / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / : / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / Ribosomal protein S27e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S3, eukaryotic/archaeal / Eukaryotic Ribosomal Protein L27, KOW domain / Elongation factor Tu domain 2 / Ribosomal Protein L6, KOW domain / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein S19e / Ribosomal protein S8e, conserved site / Ribosomal protein L27e superfamily / Ribosomal protein S19e / Ribosomal L27e protein family / Ribosomal protein L36e signature. / Ribosomal protein S8e signature. / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site Similarity search - Domain/homology
60S acidic ribosomal protein P0 / Ribosomal protein L32 / 60S ribosomal protein L36a-like / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 ...60S acidic ribosomal protein P0 / Ribosomal protein L32 / 60S ribosomal protein L36a-like / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein eL6 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Uncharacterized protein / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein eL27 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS10 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL32 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL34 / Elongation factor 2 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL37 Similarity search - Component
Biological species
Oryctolagus cuniculus (rabbit) / Homo sapiens (human) / Escherichia coli (E. coli) / Cricket paralysis virus
Method
single particle reconstruction / cryo EM / Resolution: 3.2 Å
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)
GM097014
United States
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
Deposition
Apr 30, 2018
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Header (metadata) release
Jun 6, 2018
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Map release
Jun 6, 2018
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Update
Dec 25, 2024
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Current status
Dec 25, 2024
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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