+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 / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex ...positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / exit from mitosis / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / laminin receptor activity / optic nerve development / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / retinal ganglion cell axon guidance / NF-kappaB complex / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / 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 / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / Protein hydroxylation / TOR signaling / BH3 domain binding / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Peptide chain elongation / Selenocysteine synthesis / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / gastrulation / 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) / spindle assembly / regulation of translational fidelity / MDM2/MDM4 family protein binding / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / rough endoplasmic reticulum / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / negative regulation of smoothened signaling pathway / rescue of stalled ribosome / signaling adaptor activity / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / stress granule assembly / translation initiation factor binding / maturation of SSU-rRNA / positive regulation of intrinsic apoptotic signaling pathway / Mitotic Prometaphase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / EML4 and NUDC in mitotic spindle formation / positive regulation of apoptotic signaling pathway 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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