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Yorodumi- EMDB-21529: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-I... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21529 | |||||||||
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Title | Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) | |||||||||
Map data | Sharpened map after post processing | |||||||||
Sample |
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Keywords | CrPV 5'-UTR IRES / Internal ribosome entry site / RIBOSOME / Ribosome-TRANSLATION complex | |||||||||
Function / homology | Function and homology information viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / metal-dependent deubiquitinase activity / regulation of translational initiation / laminin receptor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / translation regulator activity / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor binding / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / positive regulation of apoptotic signaling pathway / 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 / placenta development / small-subunit processome / positive regulation of translation / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / PML body / fibrillar center / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / metallopeptidase activity / glucose homeostasis / virus receptor activity / ribosome binding / 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 / cytosolic small ribosomal subunit / perikaryon / cysteine-type deubiquitinase activity / cytoplasmic translation / cell differentiation / postsynaptic density / rRNA binding / mitochondrial inner membrane / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / cell division / DNA repair / centrosome / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / negative regulation of apoptotic process / nucleolus / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Cricket paralysis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
Authors | Neupane R / Pisareva V | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2020 Title: A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate. Authors: Ritam Neupane / Vera P Pisareva / Carlos F Rodriguez / Andrey V Pisarev / Israel S Fernández / Abstract: Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have ...Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have evolved. The initiation stage of translation is especially targeted as it involves multiple steps and the engagement of numerous initiation factors. The use of structured RNA sequences, called nternal ibosomal ntry ites (IRES), in viral RNAs is a widespread strategy for the exploitation of eukaryotic initiation. Using a combination of electron cryo-microscopy (cryo-EM) and reconstituted translation initiation assays with native components, we characterized how a novel IRES at the 5'-UTR of a viral RNA assembles a functional initiation complex via an uAUG intermediate. The IRES features a novel extended, multi-domain architecture, that circles the 40S head. The structures and accompanying functional data illustrate the importance of 5'-UTR regions in translation regulation and underline the relevance of the untapped diversity of viral IRESs. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21529.map.gz | 26.9 MB | EMDB map data format | |
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Header (meta data) | emd-21529-v30.xml emd-21529.xml | 64.5 KB 64.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21529_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_21529.png | 65.8 KB | ||
Masks | emd_21529_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-21529.cif.gz | 15.4 KB | ||
Others | emd_21529_additional.map.gz emd_21529_half_map_1.map.gz emd_21529_half_map_2.map.gz | 193.5 MB 23.9 MB 23.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21529 | HTTPS FTP |
-Validation report
Summary document | emd_21529_validation.pdf.gz | 676.1 KB | Display | EMDB validaton report |
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Full document | emd_21529_full_validation.pdf.gz | 675.7 KB | Display | |
Data in XML | emd_21529_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_21529_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21529 | HTTPS FTP |
-Related structure data
Related structure data | 6w2sMC 6w2tC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21529.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map after post processing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0605 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_21529_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map before post-processing
File | emd_21529_additional.map | ||||||||||||
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Annotation | Unsharpened map before post-processing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_21529_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_21529_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-I...
+Supramolecule #1: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-I...
+Macromolecule #1: 18S rRNA
+Macromolecule #2: CrPV 5'-UTR IRES
+Macromolecule #3: uS2
+Macromolecule #4: eS1
+Macromolecule #5: uS5
+Macromolecule #6: eS4
+Macromolecule #7: eS6
+Macromolecule #8: eS7
+Macromolecule #9: eS8
+Macromolecule #10: uS4
+Macromolecule #11: uS17
+Macromolecule #12: uS15
+Macromolecule #13: uS11
+Macromolecule #14: eS21
+Macromolecule #15: uS8
+Macromolecule #16: uS12
+Macromolecule #17: eS24
+Macromolecule #18: eS26
+Macromolecule #19: eS27
+Macromolecule #20: eS30
+Macromolecule #21: uS3
+Macromolecule #22: uS7
+Macromolecule #23: eS10
+Macromolecule #24: eS12
+Macromolecule #25: uS19
+Macromolecule #26: uS9
+Macromolecule #27: eS17
+Macromolecule #28: uS13
+Macromolecule #29: eS19
+Macromolecule #30: uS10
+Macromolecule #31: eS25
+Macromolecule #32: eS28
+Macromolecule #33: eS29
+Macromolecule #34: eS31
+Macromolecule #35: RACK1
+Macromolecule #36: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #37: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #38: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #39: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #40: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #41: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #42: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #43: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #44: MAGNESIUM ION
+Macromolecule #45: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: Grids were blotted for 2.5s and flash cooled in liquid ethane. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Average exposure time: 8.0 sec. / Average electron dose: 56.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |