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Yorodumi- EMDB-21530: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-I... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21530 | |||||||||
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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 closed state (Class 2) | |||||||||
Map data | Sharpened map after post processing for Class 2 (closed) | |||||||||
Sample |
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Keywords | CrPV 5'-UTR IRES / Internal ribosome entry site / RIBOSOME | |||||||||
Function / homology | Function and homology information viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / ribosomal subunit / mammalian oogenesis stage / metal-dependent deubiquitinase activity / activation-induced cell death of T cells / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / T cell proliferation involved in immune response / erythrocyte development / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / TOR signaling / ribosomal small subunit export from nucleus / translation regulator activity / 90S preribosome / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / translation initiation factor binding / translation initiation factor activity / rescue of stalled 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) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / positive regulation of apoptotic signaling pathway / positive regulation of translation / small-subunit processome / placenta development / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / fibrillar center / PML body / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / spindle / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / metallopeptidase activity / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / positive regulation of canonical Wnt signaling pathway / rhythmic process / ribosome binding / glucose homeostasis / regulation of translation / T cell differentiation in thymus / cell body / small ribosomal subunit / cytosolic small ribosomal subunit / perikaryon / cysteine-type deubiquitinase activity / cytoplasmic translation / mitochondrial inner membrane / 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 / mRNA binding / centrosome / apoptotic process / synapse / ubiquitin protein ligase binding / 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 / nucleoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Cricket paralysis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 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_21530.map.gz | 25.9 MB | EMDB map data format | |
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Header (meta data) | emd-21530-v30.xml emd-21530.xml | 66.3 KB 66.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21530_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_21530.png | 67.2 KB | ||
Masks | emd_21530_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-21530.cif.gz | 15.9 KB | ||
Others | emd_21530_additional.map.gz emd_21530_half_map_1.map.gz emd_21530_half_map_2.map.gz | 193.4 MB 193.6 MB 193.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21530 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21530 | HTTPS FTP |
-Related structure data
Related structure data | 6w2tMC 6w2sC C: citing same article (ref.) M: atomic model generated by this map |
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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_21530.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 for Class 2 (closed) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_21530_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map before post-processing for Class 2 (closed)
File | emd_21530_additional.map | ||||||||||||
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Annotation | Unsharpened map before post-processing for Class 2 (closed) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 for Class 2 (closed)
File | emd_21530_half_map_1.map | ||||||||||||
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Annotation | Half map 2 for Class 2 (closed) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 for Class 2 (closed)
File | emd_21530_half_map_2.map | ||||||||||||
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Annotation | Half map 1 for Class 2 (closed) | ||||||||||||
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 #44: CrPV 5'-UTR IRES
+Macromolecule #2: uS2
+Macromolecule #3: eS1
+Macromolecule #4: uS5
+Macromolecule #5: eS4
+Macromolecule #6: eS6
+Macromolecule #7: eS7
+Macromolecule #8: eS8
+Macromolecule #9: uS4
+Macromolecule #10: uS17
+Macromolecule #11: uS15
+Macromolecule #12: uS11
+Macromolecule #13: eS21
+Macromolecule #14: uS8
+Macromolecule #15: uS12
+Macromolecule #16: eS24
+Macromolecule #17: eS26
+Macromolecule #18: eS27
+Macromolecule #19: eS30
+Macromolecule #20: uS3
+Macromolecule #21: uS7
+Macromolecule #22: eS10
+Macromolecule #23: eS12
+Macromolecule #24: uS19
+Macromolecule #25: uS9
+Macromolecule #26: eS17
+Macromolecule #27: uS13
+Macromolecule #28: eS19
+Macromolecule #29: uS10
+Macromolecule #30: eS25
+Macromolecule #31: eS28
+Macromolecule #32: eS29
+Macromolecule #33: eS31
+Macromolecule #34: RACK1
+Macromolecule #35: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #36: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #37: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #38: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #39: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #40: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #41: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #42: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #43: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #45: MAGNESIUM ION
+Macromolecule #46: 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |