+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3019 | |||||||||
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Title | Structure of HCV IRES bound to the human ribosome | |||||||||
Map data | Reconstruction of hepatitis C virus IRES bound to human ribosome | |||||||||
Sample |
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Keywords | Human ribosome / IRES / Hepatitis C virus / translation initiation | |||||||||
Function / homology | Function and homology information positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / protein tyrosine kinase inhibitor activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / positive regulation of endodeoxyribonuclease activity / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / oxidized purine DNA binding / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / exit from mitosis / laminin receptor activity / pigmentation / protein kinase A binding / optic nerve development / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / retinal ganglion cell axon guidance / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / iron-sulfur cluster binding / monocyte chemotaxis / positive regulation of activated T cell proliferation / Protein hydroxylation / regulation of cell division / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / regulation of translational fidelity / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / erythrocyte development / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / positive regulation of cell cycle / translation regulator activity / signaling adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of smoothened signaling pathway / stress granule assembly / Mitotic Prometaphase / laminin binding / antiviral innate immune response / EML4 and NUDC in mitotic spindle formation / cytosolic ribosome / rough endoplasmic reticulum / 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) / positive regulation of JUN kinase activity / gastrulation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Hepatitis C virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Quade N / Leibundgut M / Boehringer D / van den Heuvel J / Ban N | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Cryo-EM structure of Hepatitis C virus IRES bound to the human ribosome at 3.9-Å resolution. Authors: Nick Quade / Daniel Boehringer / Marc Leibundgut / Joop van den Heuvel / Nenad Ban / Abstract: Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation ...Hepatitis C virus (HCV), a widespread human pathogen, is dependent on a highly structured 5'-untranslated region of its mRNA, referred to as internal ribosome entry site (IRES), for the translation of all of its proteins. The HCV IRES initiates translation by directly binding to the small ribosomal subunit (40S), circumventing the need for many eukaryotic translation initiation factors required for mRNA scanning. Here we present the cryo-EM structure of the human 40S ribosomal subunit in complex with the HCV IRES at 3.9 Å resolution, determined by focused refinement of an 80S ribosome-HCV IRES complex. The structure reveals the molecular details of the interactions between the IRES and the 40S, showing that expansion segment 7 (ES7) of the 18S rRNA acts as a central anchor point for the HCV IRES. The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs. | |||||||||
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_3019.map.gz | 7.1 MB | EMDB map data format | |
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Header (meta data) | emd-3019-v30.xml emd-3019.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_3019.png | 201.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3019 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3019 | HTTPS FTP |
-Validation report
Summary document | emd_3019_validation.pdf.gz | 241.7 KB | Display | EMDB validaton report |
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Full document | emd_3019_full_validation.pdf.gz | 240.9 KB | Display | |
Data in XML | emd_3019_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3019 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3019 | HTTPS FTP |
-Related structure data
Related structure data | 5a2qMC 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_3019.map.gz / Format: CCP4 / Size: 37.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of hepatitis C virus IRES bound to human ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Hepatitis C virus IRES bound to human ribosome
Entire | Name: Hepatitis C virus IRES bound to human ribosome |
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Components |
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-Supramolecule #1000: Hepatitis C virus IRES bound to human ribosome
Supramolecule | Name: Hepatitis C virus IRES bound to human ribosome / type: sample / ID: 1000 / Oligomeric state: IRES bound to ribosome / Number unique components: 2 |
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Molecular weight | Theoretical: 1.45 MDa |
-Supramolecule #1: 40S ribosome
Supramolecule | Name: 40S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S, SSU RNA 18S |
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Ref GO | 0: GO:0005840 |
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: HEK293-6E / Location in cell: Cytosole |
Molecular weight | Theoretical: 1.35 MDa |
-Macromolecule #1: Hepatitis-C virus IRES
Macromolecule | Name: Hepatitis-C virus IRES / type: rna / ID: 1 / Name.synonym: HCV IRES / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: Hepatitis C virus |
Molecular weight | Theoretical: 100 KDa |
Sequence | String: CTCCCCTGTG AGGAACTACT GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA GCCTCCAGGA CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GGAATTGCCA GGACGACCGG GTCCTTTCTT GGATAAACCC ...String: CTCCCCTGTG AGGAACTACT GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA GCCTCCAGGA CCCCCCCTCC CGGGAGAGCC ATAGTGGTCT GCGGAACCGG TGAGTACACC GGAATTGCCA GGACGACCGG GTCCTTTCTT GGATAAACCC GCTCAATGCC TGGAGATTTG GGCGTGCCCC CGCAAGACTG CTAGCCGAGT AGTGTTGGGT CGCGAAAGGC CTTGTGGTAC TGCCTGATAG GGTGCTTGCG AGTGCCCCGG GAGGTCTCGT AGACCGTGCA CCATGAGCAC AAATC |