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Yorodumi- EMDB-25543: Structure of the wt IRES eIF5B-containing 48S initiation complex,... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25543 | |||||||||||||||
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Title | Structure of the wt IRES eIF5B-containing 48S initiation complex, closed conformation. Structure 15(wt) | |||||||||||||||
Map data | Post processed map | |||||||||||||||
Sample |
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Function / homology | Function and homology information multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells ...multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / phagocytic cup / ubiquitin ligase inhibitor activity / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / translation regulator activity / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / ribosome assembly / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / glucose homeostasis / virus receptor activity / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / cell differentiation / tRNA binding / postsynaptic density / rRNA binding / mitochondrial inner membrane / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / cell division / DNA repair / GTPase activity / centrosome / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / negative regulation of apoptotic process / nucleolus / GTP binding / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / mitochondrion / DNA binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / rabbit (rabbit) / Hepatitis C virus (isolate 1) / Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
Authors | Brown ZP / Abaeva IS / De S / Hellen CUT / Pestova TV / Frank J | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: EMBO J / Year: 2022 Title: Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES. Authors: Zuben P Brown / Irina S Abaeva / Swastik De / Christopher U T Hellen / Tatyana V Pestova / Joachim Frank / Abstract: Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical ...Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25543.map.gz | 222.1 MB | EMDB map data format | |
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Header (meta data) | emd-25543-v30.xml emd-25543.xml | 61.6 KB 61.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25543_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_25543.png | 33.6 KB | ||
Masks | emd_25543_msk_1.map | 244.1 MB | Mask map | |
Others | emd_25543_additional_1.map.gz emd_25543_additional_2.map.gz emd_25543_additional_3.map.gz emd_25543_half_map_1.map.gz emd_25543_half_map_2.map.gz | 92.6 MB 86.8 MB 192.3 MB 194 MB 192.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25543 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25543 | HTTPS FTP |
-Validation report
Summary document | emd_25543_validation.pdf.gz | 944.2 KB | Display | EMDB validaton report |
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Full document | emd_25543_full_validation.pdf.gz | 943.8 KB | Display | |
Data in XML | emd_25543_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | emd_25543_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25543 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25543 | HTTPS FTP |
-Related structure data
Related structure data | 7sywMC 7syiC 7syjC 7sykC 7sylC 7syoC 7sypC 7syqC 7syrC 7sysC 7sytC 7syuC 7syvC 7syxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25543.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Post processed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25543_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: Local resolution map filtered at local resolution
File | emd_25543_additional_1.map | ||||||||||||
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Annotation | Local resolution map filtered at local resolution | ||||||||||||
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-Additional map: Local resolution values
File | emd_25543_additional_2.map | ||||||||||||
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Annotation | Local resolution values | ||||||||||||
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-Additional map: Unsharpened map
File | emd_25543_additional_3.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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Density Histograms |
-Half map: Half map
File | emd_25543_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
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Density Histograms |
-Half map: Half map
File | emd_25543_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : 40S ribosomal small subunit with HCV IRES
+Supramolecule #1: 40S ribosomal small subunit with HCV IRES
+Macromolecule #1: 18S rRNA
+Macromolecule #36: Met-tRNA-i-Met
+Macromolecule #39: HCV IRES
+Macromolecule #2: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #3: 40S ribosomal protein SA
+Macromolecule #4: eS1
+Macromolecule #5: 40S ribosomal protein S2
+Macromolecule #6: uS3
+Macromolecule #7: 40S ribosomal protein S4
+Macromolecule #8: uS7
+Macromolecule #9: eS6
+Macromolecule #10: 40S ribosomal protein S7
+Macromolecule #11: eS8
+Macromolecule #12: uS4
+Macromolecule #13: eS10
+Macromolecule #14: uS17
+Macromolecule #15: eS12
+Macromolecule #16: uS15
+Macromolecule #17: uS11
+Macromolecule #18: uS19
+Macromolecule #19: uS9
+Macromolecule #20: eS17
+Macromolecule #21: uS13
+Macromolecule #22: eS19
+Macromolecule #23: uS10
+Macromolecule #24: 40S ribosomal protein S21
+Macromolecule #25: uS8
+Macromolecule #26: uS12
+Macromolecule #27: 40S ribosomal protein S24
+Macromolecule #28: 40S ribosomal protein S25
+Macromolecule #29: 40S ribosomal protein S26
+Macromolecule #30: eS27
+Macromolecule #31: eS28
+Macromolecule #32: eS29
+Macromolecule #33: eS30
+Macromolecule #34: 40S ribosomal protein S27a
+Macromolecule #35: RACK1
+Macromolecule #37: 60s ribosomal protein l41
+Macromolecule #38: Eukaryotic translation initiation factor 5B
+Macromolecule #40: ZINC ION
+Macromolecule #41: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #42: MAGNESIUM ION
+Macromolecule #43: SODIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.000075 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER / Details: H2/O2 mixture for 25 seconds at 25W power |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 4 second blot time, force 3. |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 4.0 sec. / Average electron dose: 70.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |