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Yorodumi- EMDB-62671: Cryo-EM structure of the HCV IRES-dependently initiated CMV-stall... -
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Basic information
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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 | |||||||||
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 / multi-eIF complex ...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 / multi-eIF complex / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / mRNA cap binding / translation at presynapse / eukaryotic 48S preinitiation complex / exit from mitosis / eukaryotic 80S initiation complex / negative regulation of protein neddylation / response to insecticide / optic nerve development / 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 / ribosomal protein import into nucleus / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / 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 / retinal ganglion cell axon guidance / positive regulation of endodeoxyribonuclease activity / IRE1-RACK1-PP2A complex / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / alpha-beta T cell differentiation / metal-dependent deubiquitinase activity / G1 to G0 transition / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / supercoiled DNA binding / neural crest cell differentiation / regulation of translational initiation / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / middle ear morphogenesis / positive regulation of ubiquitin-protein transferase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / ion channel inhibitor activity / homeostatic process / 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 / male meiosis I / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / monocyte chemotaxis / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / TOR signaling / Protein hydroxylation / BH3 domain binding / 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: 3.0 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.USA / Year: 2025Title: Structural Insights into the Role of eIF3 in Translation Mediated by the HCV IRES Authors: Iwasaki W / Kashiwagi K / Sakamoto A / Nishimoto M / Takahashi M / Machida K / Imataka H / Matsumoto A / Shichino Y / Iwasaki S / Imami K / Ito T | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_62671.map.gz | 244.8 MB | EMDB map data format | |
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| Header (meta data) | emd-62671-v30.xml emd-62671.xml | 121.5 KB 121.5 KB | Display Display | EMDB header |
| Images | emd_62671.png | 106.8 KB | ||
| Filedesc metadata | emd-62671.cif.gz | 24 KB | ||
| Others | emd_62671_additional_1.map.gz emd_62671_half_map_1.map.gz emd_62671_half_map_2.map.gz | 303 MB 383.9 MB 383.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-62671 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-62671 | HTTPS FTP |
-Validation report
| Summary document | emd_62671_validation.pdf.gz | 860.3 KB | Display | EMDB validaton report |
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| Full document | emd_62671_full_validation.pdf.gz | 859.9 KB | Display | |
| Data in XML | emd_62671_validation.xml.gz | 18.2 KB | Display | |
| Data in CIF | emd_62671_validation.cif.gz | 22.2 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-62671 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-62671 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9kzuMC ![]() 9kkfC ![]() 9kn5C ![]() 9kn6C ![]() 9krpC ![]() 9kzxC 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_62671.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_62671_additional_1.map | ||||||||||||
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| Annotation | This map was generated using refinement in RELION followed by 3DFlex refinement in cryoSPARC | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: #2
| File | emd_62671_half_map_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Half map: #1
| File | emd_62671_half_map_2.map | ||||||||||||
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| Density Histograms |
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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: 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: mRNA
+Macromolecule #82: P-site tRNA
+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 S3
+Macromolecule #50: 40S ribosomal protein S4, X isoform
+Macromolecule #51: 40S ribosomal protein S5
+Macromolecule #52: 40S ribosomal protein S7
+Macromolecule #53: 40S ribosomal protein S8
+Macromolecule #54: 40S ribosomal protein S10
+Macromolecule #55: 40S ribosomal protein S11
+Macromolecule #56: 40S ribosomal protein S15
+Macromolecule #57: 40S ribosomal protein S16
+Macromolecule #58: 40S ribosomal protein S17
+Macromolecule #59: 40S ribosomal protein S18
+Macromolecule #60: 40S ribosomal protein S19
+Macromolecule #61: 40S ribosomal protein S20
+Macromolecule #62: 40S ribosomal protein S21
+Macromolecule #63: 40S ribosomal protein S23
+Macromolecule #64: 40S ribosomal protein S26
+Macromolecule #65: 40S ribosomal protein S28
+Macromolecule #66: 40S ribosomal protein S29
+Macromolecule #67: Receptor of activated protein C kinase 1
+Macromolecule #68: 40S ribosomal protein S2
+Macromolecule #69: 40S ribosomal protein S6
+Macromolecule #70: 40S ribosomal protein S9
+Macromolecule #71: 40S ribosomal protein S12
+Macromolecule #72: 40S ribosomal protein S13
+Macromolecule #73: 40S ribosomal protein S14
+Macromolecule #74: 40S ribosomal protein S15a
+Macromolecule #75: 40S ribosomal protein S24
+Macromolecule #76: 40S ribosomal protein S25
+Macromolecule #77: 40S ribosomal protein S27
+Macromolecule #78: 40S ribosomal protein S30
+Macromolecule #79: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #81: nascent peptide
+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

