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- EMDB-20249: Structure of a mammalian small ribosomal subunit in complex with ... -
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Basic information
Entry | Database: EMDB / ID: EMD-20249 | |||||||||
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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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Function / homology | ![]() ribosomal subunit / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response ...ribosomal subunit / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cytosolic ribosome / laminin binding / 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) / gastrulation / MDM2/MDM4 family protein binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / glucose homeostasis / virus receptor activity / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / perikaryon / cytosolic small ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / cell division / DNA repair / centrosome / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Acosta-Reyes FJ / Neupane R / Frank J / Fernandez IS | |||||||||
Funding support | ![]()
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![]() | ![]() Title: 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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 54.9 KB 54.9 KB | Display Display | ![]() |
Images | ![]() | 172.5 KB | ||
Masks | ![]() | 115.9 MB | ![]() | |
Others | ![]() ![]() ![]() | 90.8 MB 91.1 MB 91.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 754.1 KB | Display | ![]() |
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Full document | ![]() | 753.6 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6p4hMC ![]() 6p4gC ![]() 6p5iC ![]() 6p5jC ![]() 6p5kC ![]() 6p5nC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.233 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: #1
File | emd_20249_additional.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_20249_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_20249_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Structure of a mammalian small ribosomal subunit in complex with ...
+Supramolecule #1: Structure of a mammalian small ribosomal subunit in complex with ...
+Macromolecule #1: 18S rRNA
+Macromolecule #6: IAPV-IRES
+Macromolecule #2: uS2
+Macromolecule #3: eS1
+Macromolecule #4: uS5
+Macromolecule #5: uS3
+Macromolecule #7: eS4
+Macromolecule #8: uS7
+Macromolecule #9: eS6
+Macromolecule #10: eS7
+Macromolecule #11: eS8
+Macromolecule #12: uS4
+Macromolecule #13: eS10
+Macromolecule #14: uS17
+Macromolecule #15: eS12
+Macromolecule #16: uS15
+Macromolecule #17: uS11
+Macromolecule #18: uS19
+Macromolecule #19: uS9
+Macromolecule #20: eS17
+Macromolecule #21: uS13
+Macromolecule #22: eS19
+Macromolecule #23: uS10
+Macromolecule #24: eS21
+Macromolecule #25: uS8
+Macromolecule #26: uS12
+Macromolecule #27: eS24
+Macromolecule #28: eS25
+Macromolecule #29: eS26
+Macromolecule #30: eS27
+Macromolecule #31: eS28
+Macromolecule #32: eS29
+Macromolecule #33: eS30
+Macromolecule #34: eS31
+Macromolecule #35: RACK1
+Macromolecule #36: eL41
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation #1
Preparation ID | 1 | ||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.33257 kPa Details: Plasma cleaning for both holey carbon and holey gold grids was done on a Gatan Solarus with Hydrogen (6.4 sccm gas flow) and Oxygen (27.5 sccm gas flow) and 10 W cleaning power. | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||
Details | Ribosomal complexes for the pre-translocated state were assembled at 240-390 nM concentration and applied to plasma treated holey carbon. |
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Sample preparation #2
Preparation ID | 2 | ||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.33257 kPa Details: Plasma cleaning for both holey carbon and holey gold grids was done on a Gatan Solarus with Hydrogen (6.4 sccm gas flow) and Oxygen (27.5 sccm gas flow) and 10 W cleaning power. | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||
Details | Same sample and buffer conditions used for the holey carbon grids was used for the holey gold grids. |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-40 / Number real images: 11234 / Average exposure time: 8.0 sec. / Average electron dose: 42.09 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 31000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |