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Yorodumi- EMDB-9703: Cryo-EM structure of the HCV IRES dependently initiated CMV-stall... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9703 | |||||||||
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Title | Cryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribosome / Translation | |||||||||
Function / homology | Function and homology information translation termination factor activity / cytoplasmic translational termination / translation release factor complex / translation release factor activity / regulation of translational termination / eukaryotic 80S initiation complex / : / translation release factor activity, codon specific / negative regulation of protein neddylation / protein methylation ...translation termination factor activity / cytoplasmic translational termination / translation release factor complex / translation release factor activity / regulation of translational termination / eukaryotic 80S initiation complex / : / translation release factor activity, codon specific / negative regulation of protein neddylation / protein methylation / translation at presynapse / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development / ribosomal protein import into nucleus / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / negative regulation of formation of translation preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / TORC2 complex binding / negative regulation of RNA splicing / negative regulation of DNA repair / sequence-specific mRNA binding / GAIT complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / oxidized purine DNA binding / NF-kappaB complex / middle ear morphogenesis / aminoacyl-tRNA hydrolase activity / neural crest cell differentiation / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / negative regulation of phagocytosis / A band / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / exit from mitosis / laminin receptor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / pigmentation / protein kinase A binding / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of ubiquitin protein ligase activity / optic nerve development / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / response to aldosterone / Translation initiation complex formation / retinal ganglion cell axon guidance / mammalian oogenesis stage / fibroblast growth factor binding / homeostatic process / positive regulation of mitochondrial depolarization / G1 to G0 transition / activation-induced cell death of T cells / macrophage chemotaxis / positive regulation of T cell receptor signaling pathway / lung morphogenesis / negative regulation of peptidyl-serine phosphorylation / iron-sulfur cluster binding / negative regulation of Wnt signaling pathway / positive regulation of activated T cell proliferation / male meiosis I / monocyte chemotaxis / Protein hydroxylation / regulation of cell division / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Yokoyama T / Shigematsu H / Shirouzu M / Imataka H / Ito T | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: Mol Cell / Year: 2019 Title: HCV IRES Captures an Actively Translating 80S Ribosome. Authors: Takeshi Yokoyama / Kodai Machida / Wakana Iwasaki / Tomoaki Shigeta / Madoka Nishimoto / Mari Takahashi / Ayako Sakamoto / Mayumi Yonemochi / Yoshie Harada / Hideki Shigematsu / Mikako ...Authors: Takeshi Yokoyama / Kodai Machida / Wakana Iwasaki / Tomoaki Shigeta / Madoka Nishimoto / Mari Takahashi / Ayako Sakamoto / Mayumi Yonemochi / Yoshie Harada / Hideki Shigematsu / Mikako Shirouzu / Hisashi Tadakuma / Hiroaki Imataka / Takuhiro Ito / Abstract: Translation initiation of hepatitis C virus (HCV) genomic RNA is induced by an internal ribosome entry site (IRES). Our cryoelectron microscopy (cryo-EM) analysis revealed that the HCV IRES binds to ...Translation initiation of hepatitis C virus (HCV) genomic RNA is induced by an internal ribosome entry site (IRES). Our cryoelectron microscopy (cryo-EM) analysis revealed that the HCV IRES binds to the solvent side of the 40S platform of the cap-dependently translating 80S ribosome. Furthermore, we obtained the cryo-EM structures of the HCV IRES capturing the 40S subunit of the IRES-dependently translating 80S ribosome. In the elucidated structures, the HCV IRES "body," consisting of domain III except for subdomain IIIb, binds to the 40S subunit, while the "long arm," consisting of domain II, remains flexible and does not impede the ongoing translation. Biochemical experiments revealed that the cap-dependently translating ribosome becomes a better substrate for the HCV IRES than the free ribosome. Therefore, the HCV IRES is likely to efficiently induce the translation initiation of its downstream mRNA with the captured translating ribosome as soon as the ongoing translation terminates. | |||||||||
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_9703.map.gz | 265 MB | EMDB map data format | |
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Header (meta data) | emd-9703-v30.xml emd-9703.xml | 99.7 KB 99.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9703_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_9703.png | 161.8 KB | ||
Filedesc metadata | emd-9703.cif.gz | 20 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9703 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9703 | HTTPS FTP |
-Validation report
Summary document | emd_9703_validation.pdf.gz | 726.1 KB | Display | EMDB validaton report |
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Full document | emd_9703_full_validation.pdf.gz | 725.7 KB | Display | |
Data in XML | emd_9703_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | emd_9703_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9703 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9703 | HTTPS FTP |
-Related structure data
Related structure data | 6ip8MC 9699C 9701C 9702C 9704C 6ip5C 6ip6C 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_9703.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.49 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Human 80S ribosome
+Supramolecule #1: Human 80S ribosome
+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 #83: P-site tRNA
+Macromolecule #84: HCV-IRES RNA
+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: 40S ribosomal protein SA
+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: Eukaryotic peptide chain release factor subunit 1
+Macromolecule #82: nascent peptide
-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 R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 33557 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 23500 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |