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Yorodumi- PDB-9kzu: Cryo-EM structure of the HCV IRES-dependently initiated CMV-stall... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9kzu | ||||||||||||||||||||||||
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| Title | Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome (non-rotated state) in complexed with eIF3 | ||||||||||||||||||||||||
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Keywords | RIBOSOME / HCV IRES | ||||||||||||||||||||||||
| Function / homology | Function and homology informationviral 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 / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex ...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 / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding / eukaryotic 48S preinitiation complex / translation at presynapse / optic nerve development / response to insecticide / alpha-beta T cell differentiation / exit from mitosis / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / negative regulation of endoplasmic reticulum unfolded protein response / regulation of G1 to G0 transition / axial mesoderm development / retinal ganglion cell axon guidance / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / middle ear morphogenesis / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / 90S preribosome assembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / regulation of translational initiation / positive regulation of ubiquitin-protein transferase activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / positive regulation of DNA-templated transcription initiation / nucleolus organization / TNFR1-mediated ceramide production / negative regulation of formation of translation preinitiation complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / PD-L1(CD274) glycosylation and translocation to plasma membrane / GAIT complex / negative regulation of RNA splicing / Enterobacterial factors antagonize host defense / TORC2 complex binding / G1 to G0 transition / metal-dependent deubiquitinase activity / supercoiled DNA binding / negative regulation of DNA repair / erythrocyte homeostasis / blastocyst development / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / NF-kappaB complex / cytoplasmic translational initiation / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of phagocytosis / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / negative regulation of myoblast fusion / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / ion channel inhibitor activity / positive regulation of natural killer cell proliferation / Maturation of DENV proteins / protein kinase A binding / homeostatic process / laminin receptor activity / lung morphogenesis / Dengue Virus Genome Translation and Replication / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Ribosomal scanning and start codon recognition / positive regulation of mitochondrial depolarization / Translation initiation complex formation / macrophage chemotaxis / negative regulation of Wnt signaling pathway / male meiosis I / fibroblast growth factor binding / Dengue Virus Attachment and Entry / Protein hydroxylation / BH3 domain binding / negative regulation of translational frameshifting / TOR signaling / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / monocyte chemotaxis / mTORC1-mediated signalling / positive regulation of GTPase activity / SARS-CoV-1 modulates host translation machinery / regulation of cell division / iron-sulfur cluster binding / cellular response to ethanol / Peptide chain elongation Similarity search - Function | ||||||||||||||||||||||||
| Biological species | Homo sapiens (human) Hepacivirus hominis | ||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 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, 2items
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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
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9kzu.cif.gz | 6.6 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9kzu.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9kzu.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/9kzu ftp://data.pdbj.org/pub/pdb/validation_reports/kz/9kzu | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 62671MC ![]() 9kkfC ![]() 9kn5C ![]() 9kn6C ![]() 9krpC ![]() 9kzxC C: citing same article ( M: map data used to model this data |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-RNA chain , 7 types, 7 molecules L5L7L8S2zvzyzz
| #1: RNA chain | Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 86475748 |
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| #2: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_023363 |
| #3: RNA chain | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: KY962518 |
| #46: RNA chain | Mass: 602777.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 2795772166 |
| #80: RNA chain | Mass: 5933.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
| #82: RNA chain | Mass: 24189.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
| #83: RNA chain | Mass: 107002.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hepacivirus hominis / References: GenBank: 221513 |
+60S ribosomal protein ... , 41 types, 41 molecules LALBLCLDLELFLGLHLILJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLe...
-Protein , 4 types, 4 molecules LmSASgsh
| #41: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987 |
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| #47: Protein | Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865 |
| #67: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244 |
| #79: Protein | Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979 |
+40S ribosomal protein ... , 30 types, 30 molecules SBSDSESFSHSISKSLSPSQSRSSSTSUSVSXSaScSdSCSGSJSfSNSOSWSYSZSbSe
-Protein/peptide , 1 types, 1 molecules zx
| #81: Protein/peptide | Mass: 3527.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Eukaryotic translation initiation factor 3 subunit ... , 9 types, 9 molecules 3m3f3a3e3c3h3d3k3l
| #84: Protein | Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7L2H7 |
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| #85: Protein | Mass: 37593.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00303, ubiquitinyl hydrolase 1 |
| #86: Protein | Mass: 166903.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14152 |
| #87: Protein | Mass: 52281.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60228 |
| #88: Protein | Mass: 105503.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99613 |
| #89: Protein | Mass: 39979.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15372 |
| #90: Protein | Mass: 64060.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15371 |
| #91: Protein | Mass: 25083.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UBQ5 |
| #92: Protein | Mass: 66803.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y262 |
-Non-polymers , 2 types, 88 molecules 


| #93: Chemical | ChemComp-MG / #94: Chemical | ChemComp-ZN / |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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| Source (natural) |
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| Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
| Image recording | Electron dose: 56.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
| EM software | Name: PHENIX / Version: 1.21.2_5419 / Category: model refinement |
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| CTF correction | Type: NONE |
| 3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63366 / Symmetry type: POINT |
| Refinement | Cross valid method: NONE |
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About Yorodumi



Homo sapiens (human)
Hepacivirus hominis
Japan, 2items
Citation










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