+Open data
-Basic information
Entry | Database: PDB / ID: 5a2q | |||||||||
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Title | Structure of the HCV IRES bound to the human ribosome | |||||||||
Components |
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Keywords | RIBOSOME / HUMAN RIBOSOME / HEPATITIS-C / IRES / 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 / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / nucleolus organization / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity / exit from mitosis / TNFR1-mediated ceramide production / negative regulation of RNA splicing ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / nucleolus organization / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity / exit from mitosis / TNFR1-mediated ceramide production / negative regulation of RNA splicing / optic nerve development / neural crest cell differentiation / retinal ganglion cell axon guidance / rRNA modification in the nucleus and cytosol / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / pigmentation / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / IRE1-RACK1-PP2A complex / ion channel inhibitor activity / positive regulation of Golgi to plasma membrane protein transport / negative regulation of DNA repair / Translation initiation complex formation / oxidized purine DNA binding / negative regulation of Wnt signaling pathway / supercoiled DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / NF-kappaB complex / negative regulation of phagocytosis / fibroblast growth factor binding / ubiquitin-like protein conjugating enzyme binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / TOR signaling / iron-sulfur cluster binding / mTORC1-mediated signalling / protein kinase A binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / monocyte chemotaxis / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / phagocytic cup / positive regulation of mitochondrial depolarization / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of T cell receptor signaling pathway / Viral mRNA Translation / positive regulation of activated T cell proliferation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of respiratory burst involved in inflammatory response / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / BH3 domain binding / 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) / regulation of translational fidelity / cysteine-type endopeptidase activator activity involved in apoptotic process / ribosomal small subunit export from nucleus / Protein methylation / Nuclear events stimulated by ALK signaling in cancer / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of cell cycle / stress granule assembly / translation initiation factor binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / maturation of SSU-rRNA / rough endoplasmic reticulum / laminin binding / Mitotic Prometaphase / gastrulation / spindle assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / EML4 and NUDC in mitotic spindle formation / positive regulation of apoptotic signaling pathway / Maturation of protein E / positive regulation of JUN kinase activity / Maturation of protein E / ER Quality Control Compartment (ERQC) / signaling adaptor activity / MDM2/MDM4 family protein binding / translational initiation Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) HEPATITIS C VIRUS | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Quade, N. / Leiundgut, M. / Boehringer, D. / Heuvel, J.v.d. / 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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5a2q.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5a2q.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 5a2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/5a2q ftp://data.pdbj.org/pub/pdb/validation_reports/a2/5a2q | HTTPS FTP |
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-Related structure data
Related structure data | 3019MC 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
-RNA chain , 2 types, 2 molecules 23
#1: RNA chain | Mass: 602432.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HEK293-6E / Organ: KIDNEY / References: GenBank: 337376 |
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#2: RNA chain | Mass: 82914.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HEPATITIS C VIRUS |
+RIBOSOMAL PROTEIN ... , 36 types, 36 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
-Non-polymers , 3 types, 245 molecules
#39: Chemical | ChemComp-MG / #40: Chemical | #41: Water | ChemComp-HOH / | |
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-Details
Sequence details | GENBANK REFERENCE FOR CHAIN A CAA54808.1 GENBANK REFERENCE FOR CHAIN G AAH27620.1 |
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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: HCV IRES BOUND TO HUMAN 80S RIBOSOME / Type: RIBOSOME |
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Buffer solution | Name: 20MM HEPES, 100 MM KCL, 5 MM MGCL2 / pH: 7.6 / Details: 20MM HEPES, 100 MM KCL, 5 MM MGCL2 |
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE Details: FROZEN ON 200 MESH QUANTIFOIL R 2 2 HOLEY CARBON GRIDS WITH A THIN CONTINUOUS CARBON SUPPORT FILM APPLIED IN ETHANE PROPANE MIX |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Nov 20, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 100719 X / Nominal defocus max: 3400 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: INDIVIDUAL FRAMES | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: MAXIMUM LIKELIHOOD BASED REFINEMENT / Resolution: 3.9 Å / Num. of particles: 404357 / Nominal pixel size: 1.39 Å / Symmetry type: POINT | ||||||||||||
Atomic model building | B value: 119.1 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: R-factor Details: METHOD--RIGID BODY REFINEMENT FOLLOWED BY MANUAL MODEL BUILDING REFINEMENT PROTOCOL--CRYO-EM | ||||||||||||
Atomic model building | PDB-ID: 4W23 4w23 | ||||||||||||
Refinement | Highest resolution: 3.9 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.9 Å
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