[English] 日本語
Yorodumi- EMDB-20255: Structure of a mammalian 80S ribosome in complex with the Israeli... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20255 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1) | |||||||||
Map data | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information ribosomal subunit / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage ...ribosomal subunit / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / 90S preribosome / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / erythrocyte development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal small subunit export from nucleus / translation regulator activity / 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 / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / positive regulation of translation / small-subunit processome / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / spindle / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / heparin binding / retina development in camera-type eye / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / T cell differentiation in thymus / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cell body / cytoplasmic translation / perikaryon / cytosolic large ribosomal subunit / defense response to Gram-negative bacterium / killing of cells of another organism / tRNA binding / mitochondrial inner membrane / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of apoptotic process / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / cell division / DNA repair / mRNA binding / centrosome / dendrite / ubiquitin protein ligase binding / positive regulation of cell population proliferation / synapse / positive regulation of gene expression / negative regulation of apoptotic process Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) / Israeli acute paralysis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Acosta-Reyes FJ / Neupane R / Frank J / Fernandez IS | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: EMBO J / Year: 2019 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20255.map.gz | 26 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-20255-v30.xml emd-20255.xml | 96.7 KB 96.7 KB | Display Display | EMDB header |
Images | emd_20255.png | 211 KB | ||
Masks | emd_20255_msk_1.map | 178 MB | Mask map | |
Others | emd_20255_additional.map.gz emd_20255_half_map_1.map.gz emd_20255_half_map_2.map.gz | 140.7 MB 141.1 MB 141.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20255 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20255 | HTTPS FTP |
-Validation report
Summary document | emd_20255_validation.pdf.gz | 825.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_20255_full_validation.pdf.gz | 824.9 KB | Display | |
Data in XML | emd_20255_validation.xml.gz | 15 KB | Display | |
Data in CIF | emd_20255_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20255 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20255 | HTTPS FTP |
-Related structure data
Related structure data | 6p5iMC 6p4gC 6p4hC 6p5jC 6p5kC 6p5nC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_20255.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.233 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_20255_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: mammalian 80S ribosome in complex with the Israeli...
File | emd_20255_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: mammalian 80S ribosome in complex with the Israeli...
File | emd_20255_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: mammalian 80S ribosome in complex with the Israeli...
File | emd_20255_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Structure of a mammalian 80S ribosome in complex with the Israeli...
+Supramolecule #1: Structure of a mammalian 80S ribosome in complex with the Israeli...
+Macromolecule #1: 18S rRNA
+Macromolecule #35: IAPV-IRES
+Macromolecule #36: 28S rRNA
+Macromolecule #37: 5S rRNA
+Macromolecule #38: 5.8S rRNA
+Macromolecule #2: uS2
+Macromolecule #3: eS1
+Macromolecule #4: uS5
+Macromolecule #5: uS3
+Macromolecule #6: eS4
+Macromolecule #7: uS7
+Macromolecule #8: eS6
+Macromolecule #9: eS7
+Macromolecule #10: eS8
+Macromolecule #11: uS4
+Macromolecule #12: eS10
+Macromolecule #13: uS17
+Macromolecule #14: eS12
+Macromolecule #15: uS15
+Macromolecule #16: uS11
+Macromolecule #17: uS19
+Macromolecule #18: uS9
+Macromolecule #19: eS17
+Macromolecule #20: uS13
+Macromolecule #21: eS19
+Macromolecule #22: uS10
+Macromolecule #23: eS21
+Macromolecule #24: uS8
+Macromolecule #25: uS12
+Macromolecule #26: eS24
+Macromolecule #27: eS25
+Macromolecule #28: eS26
+Macromolecule #29: eS27
+Macromolecule #30: eS28
+Macromolecule #31: eS29
+Macromolecule #32: eS30
+Macromolecule #33: eS31
+Macromolecule #34: RACK1
+Macromolecule #39: uL2
+Macromolecule #40: uL3
+Macromolecule #41: uL4
+Macromolecule #42: uL18
+Macromolecule #43: eL6
+Macromolecule #44: uL30
+Macromolecule #45: eL8
+Macromolecule #46: uL6
+Macromolecule #47: uL16
+Macromolecule #48: uL11
+Macromolecule #49: eL13
+Macromolecule #50: L14e
+Macromolecule #51: eL15
+Macromolecule #52: uL13
+Macromolecule #53: uL22
+Macromolecule #54: eL18
+Macromolecule #55: eL19
+Macromolecule #56: eL20
+Macromolecule #57: eL21
+Macromolecule #58: eL22
+Macromolecule #59: uL14
+Macromolecule #60: eL24
+Macromolecule #61: eL23
+Macromolecule #62: uL24
+Macromolecule #63: eL27
+Macromolecule #64: uL15
+Macromolecule #65: eL29
+Macromolecule #66: eL30
+Macromolecule #67: eL31
+Macromolecule #68: eL32
+Macromolecule #69: eL33
+Macromolecule #70: eL34
+Macromolecule #71: eL35
+Macromolecule #72: eL36
+Macromolecule #73: eL37
+Macromolecule #74: eL38
+Macromolecule #75: eL39
+Macromolecule #76: eL40
+Macromolecule #77: eL41
+Macromolecule #78: eL42
+Macromolecule #79: eL43
+Macromolecule #80: eL28
+Macromolecule #81: uL1
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / 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: Blot force = 3s Wait time = 15s Drain time = 0s Blot time = 2.5 to 3 s. | ||||||||||
Details | Ribosomal complexes for the pre-translocated state were assembled at 240-390 nM concentration and applied to plasma treated holey carbon. |
-Electron microscopy
Microscope | FEI TECNAI F30 |
---|---|
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: FIELD EMISSION GUN |
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 |