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Open data
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Basic information
| Entry | Database: PDB / ID: 9uzk | ||||||||||||||||||||||||
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| Title | EMCV IRES captured on mammalian 40S with initiator tRNA | ||||||||||||||||||||||||
Components |
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Keywords | RIBOSOME / EMCV IRES / 40S ribosome / 48S PIC | ||||||||||||||||||||||||
| Function / homology | Function and homology informationlaminin receptor activity / 90S preribosome / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / phagocytic cup / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / laminin binding / gastrulation ...laminin receptor activity / 90S preribosome / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / phagocytic cup / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / laminin binding / 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 SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA / small-subunit processome / spindle / rRNA processing / positive regulation of canonical Wnt signaling pathway / rhythmic process / regulation of translation / ribosomal small subunit assembly / virus receptor activity / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cell differentiation / cytoplasmic translation / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / apoptotic process / centrosome / synapse / dendrite / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||||||||
| Biological species | Encephalomyocarditis virus![]() | ||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||||||||||||||||||||
Authors | Das, D. / Hussain, T. | ||||||||||||||||||||||||
| Funding support | India, 1items
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Citation | Journal: Elife / Year: 2026Title: Structural insights into the recruitment of viral Type 2 IRES to ribosomal preinitiation complex for protein synthesis Authors: Das, D. / Hussain, T. | ||||||||||||||||||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9uzk.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9uzk.ent.gz | 1.4 MB | Display | PDB format |
| PDBx/mmJSON format | 9uzk.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/9uzk ftp://data.pdbj.org/pub/pdb/validation_reports/uz/9uzk | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 64644MC ![]() 9uzlC ![]() 9uzmC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 |
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Components
-RNA chain , 3 types, 3 molecules 2yz
| #1: RNA chain | Mass: 600900.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #36: RNA chain | Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #37: RNA chain | Mass: 29887.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalomyocarditis virus / Production host: ![]() |
+Small ribosomal subunit protein ... , 31 types, 31 molecules CDEFGHIJKLMNOPRSTUVWXYZbcdeghil
-Protein , 3 types, 3 molecules Qaf
| #16: Protein | Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #26: Protein | Mass: 14575.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #31: Protein | Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Details
| Has protein modification | Y |
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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 |
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Sample preparation
| Component | Name: EMCV IRES with 40S and initiator tRNA / Type: RIBOSOME Details: EMCV IRES captured in 48S PIC using affinity-based pull-down from rabbit reticulocyte lysate Entity ID: all / Source: NATURAL |
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| Molecular weight | Experimental value: NO |
| Source (natural) | Organism: ![]() |
| Buffer solution | pH: 7.4 Details: 20mM HEPES, 150mM KOAc, 2mM MgCl2, 1mM DTT, 0.5mM Spermidine, 6mM GMP-PnP |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 |
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 289 K |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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| Microscopy | Model: FEI TALOS ARCTICA |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2750 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 83 K / Temperature (min): 77 K |
| Image recording | Electron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 6 / Num. of real images: 22549 |
| Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 20 |
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Processing
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| CTF correction | Type: NONE | ||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55231 / Symmetry type: POINT | ||||||||||||||||||||||||||||
| Atomic model building | 3D fitting-ID: 1
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About Yorodumi




Encephalomyocarditis virus

India, 1items
Citation




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FIELD EMISSION GUN

