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Yorodumi- EMDB-62679: Cryo-EM structure of the HCV IRES-dependently initiated CMV-stall... -
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Open data
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Basic information
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| Title | Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome (rotated state) in complexed with eIF3 | |||||||||
Map data | For modeling, focused map of eIF3 and the map generated by 3DFlex refinement in cryoSPARC, deposited as an additional map were used. | |||||||||
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Keywords | HCV IRES / RIBOSOME | |||||||||
| Function / homology | Function and homology informationpositive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / cytoplasmic translational initiation ...positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / cytoplasmic translational initiation / multi-eIF complex / eukaryotic 43S preinitiation complex / mRNA cap binding / translation at presynapse / eukaryotic 48S preinitiation complex / exit from mitosis / optic nerve development / response to insecticide / eukaryotic 80S initiation complex / negative regulation of protein neddylation / regulation of translation involved in cellular response to UV / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of base-excision repair / ribosomal protein import into nucleus / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / 90S preribosome assembly / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / nucleolus organization / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / metal-dependent deubiquitinase activity / alpha-beta T cell differentiation / negative regulation of DNA repair / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of RNA splicing / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / regulation of translational initiation / TORC2 complex binding / G1 to G0 transition / supercoiled DNA binding / NF-kappaB complex / neural crest cell differentiation / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / positive regulation of ubiquitin-protein transferase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / laminin receptor activity / homeostatic process / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / macrophage chemotaxis / lung morphogenesis / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / male meiosis I / monocyte chemotaxis / TOR signaling / negative regulation of translational frameshifting / BH3 domain binding / positive regulation of activated T cell proliferation / Protein hydroxylation / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) / Hepacivirus hominis | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Iwasaki W / Kashiwagi K / Sakamoto A / Nishimoto M / Takahashi M / Machida K / Imataka H / Matsumoto A / Shichino Y / Iwasaki S ...Iwasaki W / Kashiwagi K / Sakamoto A / Nishimoto M / Takahashi M / Machida K / Imataka H / Matsumoto A / Shichino Y / Iwasaki S / Imami K / Ito T | |||||||||
| Funding support | Japan, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2025Title: Structural insights into the role of eIF3 in translation mediated by the HCV IRES. Authors: Wakana Iwasaki / Kazuhiro Kashiwagi / Ayako Sakamoto / Madoka Nishimoto / Mari Takahashi / Kodai Machida / Hiroaki Imataka / Akinobu Matsumoto / Yuichi Shichino / Shintaro Iwasaki / Koshi Imami / Takuhiro Ito / ![]() Abstract: The genomes of various RNA viruses and a subset of human genes contain structured RNA elements termed internal ribosomal entry sites (IRESs) to initiate translation in a cap-independent manner. The ...The genomes of various RNA viruses and a subset of human genes contain structured RNA elements termed internal ribosomal entry sites (IRESs) to initiate translation in a cap-independent manner. The well-studied IRES from Hepatitis C virus (HCV) binds to eukaryotic initiation factor 3 (eIF3), but how the HCV IRES harnesses eIF3 for viral translation remains unclear. Here, we determined multiple cryo-EM structures in which the HCV IRES binds simultaneously to the ribosome and eIF3, covering steps from initiation to elongation. The eIF3 core subunits are displaced from the ribosome by binding more tightly to subdomain IIIb of the HCV IRES. However, cross-linking mass spectrometry suggested that the eIF3 noncore subunits in the HCV-IRES-mediated elongation complex remain in similar positions on the ribosome to those observed in the cap-mediated initiation complex. This currently determined configuration of eIF3 core and noncore subunits reveals the mechanisms through which the HCV IRES overcomes the competition with the host mRNA and promotes viral mRNA translation by utilizing eIF3. Interestingly, cryo-EM structures also revealed that the N-terminal domain of the eIF3 c-subunit (eIF3c-NTD) binds to the large ribosomal subunit (60S) during elongation. These findings suggest that eIF3 contributes to HCV IRES-mediated translation not only during initiation but also elongation and potentially in reinitiation. The interaction between the eIF3c-NTD and the 60S ribosome is likely to occur in general translation processes as well, contributing to 60S joining or eIF3 stabilization on the elongating ribosome. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_62679.map.gz | 244.3 MB | EMDB map data format | |
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| Header (meta data) | emd-62679-v30.xml emd-62679.xml | 135.9 KB 135.9 KB | Display Display | EMDB header |
| Images | emd_62679.png | 107 KB | ||
| Filedesc metadata | emd-62679.cif.gz | 24.3 KB | ||
| Others | emd_62679_additional_1.map.gz emd_62679_half_map_1.map.gz emd_62679_half_map_2.map.gz | 302.8 MB 383.5 MB 381.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-62679 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-62679 | HTTPS FTP |
-Validation report
| Summary document | emd_62679_validation.pdf.gz | 1022.5 KB | Display | EMDB validaton report |
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| Full document | emd_62679_full_validation.pdf.gz | 1022.1 KB | Display | |
| Data in XML | emd_62679_validation.xml.gz | 18.3 KB | Display | |
| Data in CIF | emd_62679_validation.cif.gz | 22.2 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-62679 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-62679 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9kzxMC ![]() 9kkfC ![]() 9kn5C ![]() 9kn6C ![]() 9krpC ![]() 9kzuC 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_62679.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | For modeling, focused map of eIF3 and the map generated by 3DFlex refinement in cryoSPARC, deposited as an additional map were used. | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.484 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: This map was generated using refinement in RELION...
| File | emd_62679_additional_1.map | ||||||||||||
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| Annotation | This map was generated using refinement in RELION followed by 3DFlex refinement in cryoSPARC. | ||||||||||||
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| Density Histograms |
-Half map: #2
| File | emd_62679_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_62679_half_map_2.map | ||||||||||||
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Sample components
+Entire : HCV IRES-dependently initiated CMV-stalled 80S ribosome (non-rota...
+Supramolecule #1: HCV IRES-dependently initiated CMV-stalled 80S ribosome (non-rota...
+Supramolecule #2: Eukaryotic translation initiation factor 3
+Supramolecule #3: ribosome
+Supramolecule #4: HCV IRES
+Macromolecule #1: 28S ribosomal RNA
+Macromolecule #2: 5S_ribosomal_RNA
+Macromolecule #3: 5.8S_ribosomal_RNA
+Macromolecule #46: 18S ribosomal RNA
+Macromolecule #80: tRNA
+Macromolecule #81: mRNA
+Macromolecule #83: HCV IRES
+Macromolecule #4: 60S ribosomal protein L8
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6
+Macromolecule #9: 60S ribosomal protein L7
+Macromolecule #10: 60S ribosomal protein L7a
+Macromolecule #11: 60S ribosomal protein L9
+Macromolecule #12: 60S ribosomal protein L10-like
+Macromolecule #13: 60S ribosomal protein L11
+Macromolecule #14: 60S ribosomal protein L13
+Macromolecule #15: 60S ribosomal protein L14
+Macromolecule #16: 60S ribosomal protein L15
+Macromolecule #17: 60S ribosomal protein L13a
+Macromolecule #18: 60S ribosomal protein L17
+Macromolecule #19: 60S ribosomal protein L18
+Macromolecule #20: 60S ribosomal protein L19
+Macromolecule #21: 60S ribosomal protein L18a
+Macromolecule #22: 60S ribosomal protein L21
+Macromolecule #23: 60S ribosomal protein L22
+Macromolecule #24: 60S ribosomal protein L23
+Macromolecule #25: 60S ribosomal protein L24
+Macromolecule #26: 60S ribosomal protein L23a
+Macromolecule #27: 60S ribosomal protein L26
+Macromolecule #28: 60S ribosomal protein L27
+Macromolecule #29: 60S ribosomal protein L27a
+Macromolecule #30: 60S ribosomal protein L29
+Macromolecule #31: 60S ribosomal protein L30
+Macromolecule #32: 60S ribosomal protein L31
+Macromolecule #33: 60S ribosomal protein L32
+Macromolecule #34: 60S ribosomal protein L35a
+Macromolecule #35: 60S ribosomal protein L34
+Macromolecule #36: 60S ribosomal protein L35
+Macromolecule #37: 60S ribosomal protein L36
+Macromolecule #38: 60S ribosomal protein L37
+Macromolecule #39: 60S ribosomal protein L38
+Macromolecule #40: 60S ribosomal protein L39
+Macromolecule #41: Ubiquitin-60S ribosomal protein L40
+Macromolecule #42: 60S ribosomal protein L41
+Macromolecule #43: 60S ribosomal protein L36a
+Macromolecule #44: 60S ribosomal protein L37a
+Macromolecule #45: 60S ribosomal protein L28
+Macromolecule #47: Small ribosomal subunit protein uS2
+Macromolecule #48: 40S ribosomal protein S3a
+Macromolecule #49: 40S ribosomal protein S2
+Macromolecule #50: 40S ribosomal protein S3
+Macromolecule #51: 40S ribosomal protein S4, X isoform
+Macromolecule #52: 40S ribosomal protein S5
+Macromolecule #53: 40S ribosomal protein S6
+Macromolecule #54: 40S ribosomal protein S7
+Macromolecule #55: 40S ribosomal protein S8
+Macromolecule #56: 40S ribosomal protein S9
+Macromolecule #57: 40S ribosomal protein S10
+Macromolecule #58: 40S ribosomal protein S11
+Macromolecule #59: 40S ribosomal protein S13
+Macromolecule #60: 40S ribosomal protein S14
+Macromolecule #61: 40S ribosomal protein S15
+Macromolecule #62: 40S ribosomal protein S16
+Macromolecule #63: 40S ribosomal protein S17
+Macromolecule #64: 40S ribosomal protein S18
+Macromolecule #65: 40S ribosomal protein S19
+Macromolecule #66: 40S ribosomal protein S20
+Macromolecule #67: 40S ribosomal protein S21
+Macromolecule #68: 40S ribosomal protein S15a
+Macromolecule #69: 40S ribosomal protein S23
+Macromolecule #70: 40S ribosomal protein S24
+Macromolecule #71: 40S ribosomal protein S25
+Macromolecule #72: 40S ribosomal protein S26
+Macromolecule #73: 40S ribosomal protein S27
+Macromolecule #74: 40S ribosomal protein S28
+Macromolecule #75: 40S ribosomal protein S29
+Macromolecule #76: 40S ribosomal protein S30
+Macromolecule #77: 40S ribosomal protein S12
+Macromolecule #78: Receptor of activated protein C kinase 1
+Macromolecule #79: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #82: nascent chain
+Macromolecule #84: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #85: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #86: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #87: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #88: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #89: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #90: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #91: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #92: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #93: MAGNESIUM ION
+Macromolecule #94: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.2 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Hepacivirus hominis
Authors
Japan, 2 items
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Processing
FIELD EMISSION GUN

