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Yorodumi- EMDB-40774: Structure of the 48S translation initiation complex assembled on ... -
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Open data
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Basic information
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| Title | Structure of the 48S translation initiation complex assembled on the encephalomyocarditis virus IRES | ||||||||||||||||||
Map data | 40SIC-EMCV-tRNA-eIF3 | ||||||||||||||||||
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Keywords | EMCV / IRES / Cryo-EM / 40SIC / RIBOSOME | ||||||||||||||||||
| Function / homology | Function and homology informationviral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / metal-dependent deubiquitinase activity / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / phagocytic cup / translation regulator activity / rough endoplasmic reticulum / laminin binding / ribosomal small subunit export from nucleus / translation initiation factor binding / translation initiation factor 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 translation / ribosome assembly / 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 / translational initiation / PML body / spindle / fibrillar center / metallopeptidase activity / rRNA processing / positive regulation of canonical Wnt signaling pathway / rhythmic process / regulation of translation / ribosomal small subunit assembly / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cell differentiation / cytoplasmic translation / tRNA binding / cysteine-type deubiquitinase activity / 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 / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
| Biological species | ![]() Encephalomyocarditis virus / Homo sapiens (human) | ||||||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Bhattacharjee S / Abaeva IS / Brown ZP / Arhab Y / Fallah H / Jeevan JC / Hellen CUT / Frank J / Pestova TV | ||||||||||||||||||
| Funding support | United States, 5 items
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Citation | Journal: bioRxiv / Year: 2025Title: The mechanism of ribosomal recruitment during translation initiation on Type 2 IRESs. Authors: Sayan Bhattacharjee / Irina S Abaeva / Zuben P Brown / Yani Arhab / Hengameh Fallah / Christopher U T Hellen / Joachim Frank / Tatyana V Pestova / ![]() Abstract: The encephalomyocarditis virus (EMCV) IRES and other Type 2 IRESs comprise domains H-L and specifically interact with eIF4G/eIF4A through their essential JK domain. However, the JK domain is not ...The encephalomyocarditis virus (EMCV) IRES and other Type 2 IRESs comprise domains H-L and specifically interact with eIF4G/eIF4A through their essential JK domain. However, the JK domain is not sufficient for IRES function, which also requires the preceding domain I of unknown function. To identify interactions that drive ribosomal recruitment of eIF4G/eIF4A-bound Type 2 IRESs, we determined the cryo-EM structure of 48S initiation complexes formed on the EMCV IRES. It revealed that the apical domain I cloverleaf contacts ribosomal proteins uS13 and uS19 via its Id subdomain and that the essential GNRA tetraloop in subdomain Ic interacts directly with the TψC domain of initiator tRNA. Functional assays supported the exceptional role of these interactions for initiation on this IRES. The strong conservation of primary and secondary structures of the apex of domain I among Type 2 IRESs suggests that the reported interactions are a common essential feature of them all. | ||||||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_40774.map.gz | 111.1 MB | EMDB map data format | |
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| Header (meta data) | emd-40774-v30.xml emd-40774.xml | 78.1 KB 78.1 KB | Display Display | EMDB header |
| Images | emd_40774.png | 93.8 KB | ||
| Filedesc metadata | emd-40774.cif.gz | 16.2 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40774 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40774 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8supMC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_40774.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | 40SIC-EMCV-tRNA-eIF3 | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : EMCV IRES 40SIC
+Supramolecule #1: EMCV IRES 40SIC
+Supramolecule #2: 40SIC
+Supramolecule #3: EMCV IRES
+Macromolecule #1: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #2: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #3: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #4: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #5: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #6: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #7: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #8: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #11: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #12: uS2 (SA)
+Macromolecule #13: eS1
+Macromolecule #14: 40S ribosomal protein S2
+Macromolecule #15: uS3
+Macromolecule #16: eS4 (S4 X isoform)
+Macromolecule #17: uS7
+Macromolecule #18: eS6
+Macromolecule #19: eS7
+Macromolecule #20: eS8
+Macromolecule #21: uS4
+Macromolecule #22: eS10
+Macromolecule #23: uS17
+Macromolecule #24: eS12
+Macromolecule #25: uS15
+Macromolecule #26: Small ribosomal subunit protein uS11
+Macromolecule #27: uS19
+Macromolecule #28: uS9
+Macromolecule #29: eS17
+Macromolecule #30: uS13
+Macromolecule #31: eS19
+Macromolecule #32: uS10
+Macromolecule #33: eS21
+Macromolecule #34: uS8
+Macromolecule #35: uS12
+Macromolecule #36: eS24
+Macromolecule #37: eS25
+Macromolecule #38: eS26
+Macromolecule #39: eS27
+Macromolecule #40: eS28
+Macromolecule #41: uS14
+Macromolecule #42: eS30
+Macromolecule #43: eS31
+Macromolecule #44: Receptor for Activated C Kinase 1 (RACK1)
+Macromolecule #46: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #47: eL41
+Macromolecule #9: 18S rRNA
+Macromolecule #10: EMCV mRNA
+Macromolecule #45: Met-tRNAiMet
+Macromolecule #48: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | cell |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TECNAI F30 |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Encephalomyocarditis virus
Homo sapiens (human)
Authors
United States, 5 items
Citation












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Processing
FIELD EMISSION GUN
