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Yorodumi- PDB-6p4h: Structure of a mammalian small ribosomal subunit in complex with ... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 6p4h | ||||||
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| Title | Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2) | ||||||
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Keywords | RIBOSOME / Israeli Acute Paralysis Virus / Internal Ribosome Entry Site / IRES / Small Ribosomal Subunit / 40S | ||||||
| Function / homology | Function and homology informationribosomal subunit / laminin receptor activity / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / laminin binding / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / translation regulator activity ...ribosomal subunit / laminin receptor activity / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / 90S preribosome / phagocytic cup / laminin binding / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / 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 / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / spindle / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / regulation of translation / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / cell differentiation / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / apoptotic process / synapse / dendrite / centrosome / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / nucleus / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
| Biological species | Israeli acute paralysis virus![]() | ||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Acosta-Reyes, F.J. / Neupane, R. / Frank, J. / Fernandez, I.S. | ||||||
| Funding support | United States, 1items
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Citation | Journal: EMBO J / Year: 2019Title: The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs. Authors: Francisco Acosta-Reyes / Ritam Neupane / Joachim Frank / Israel S Fernández / ![]() Abstract: Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a ...Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches. | ||||||
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Structure visualization
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| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6p4h.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb6p4h.ent.gz | 1.5 MB | Display | PDB format |
| PDBx/mmJSON format | 6p4h.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6p4h_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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| Full document | 6p4h_full_validation.pdf.gz | 1.6 MB | Display | |
| Data in XML | 6p4h_validation.xml.gz | 150.7 KB | Display | |
| Data in CIF | 6p4h_validation.cif.gz | 250.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/6p4h ftp://data.pdbj.org/pub/pdb/validation_reports/p4/6p4h | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 20249MC ![]() 6p4gC ![]() 6p5iC ![]() 6p5jC ![]() 6p5kC ![]() 6p5nC C: citing same article ( M: map data used to model this data |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-RNA chain , 2 types, 2 molecules 21
| #1: RNA chain | Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #6: RNA chain | Mass: 81572.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Israeli acute paralysis virus / Production host: synthetic construct (others) / References: GenBank: 124494152 |
+Protein , 33 types, 33 molecules BCDEFGHIJKLMNOPQRSTUVWXYZabcde...
-Protein/peptide , 1 types, 1 molecules n
| #36: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-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: Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2) Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||
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| Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
| Source (natural) | Organism: ![]() | ||||||||||||||||||||||||
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| Vitrification |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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| Microscopy | Model: FEI TECNAI F30 |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 31000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.26 mm |
| Specimen holder | Cryogen: NITROGEN |
| Image recording | Average exposure time: 8 sec. / Electron dose: 42.09 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 11234 |
| Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 40 / Used frames/image: 1-40 |
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Processing
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
| Particle selection | Num. of particles selected: 1240275 | |||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
| 3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96826 / Symmetry type: POINT |
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About Yorodumi



Israeli acute paralysis virus

United States, 1items
Citation
UCSF Chimera




















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