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Yorodumi- EMDB-25539: Structure of the delta dII IRES eIF2-containing 48S initiation co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25539 | ||||||||||||
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Title | Structure of the delta dII IRES eIF2-containing 48S initiation complex, closed conformation. Structure 12(delta dII). | ||||||||||||
Map data | Post processed map | ||||||||||||
Sample |
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Function / homology | Function and homology information regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency ...regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / PERK regulates gene expression / regulation of translational initiation in response to stress / eukaryotic translation initiation factor 2 complex / multi-eIF complex / translation factor activity, RNA binding / ribosomal subunit / eukaryotic 43S preinitiation complex / 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 / ubiquitin ligase inhibitor activity / phagocytic cup / Response of EIF2AK4 (GCN2) to amino acid deficiency / mitophagy / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / erythrocyte development / ribosomal small subunit export from nucleus / translation regulator activity / stress granule assembly / laminin binding / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / response to endoplasmic reticulum stress / translation initiation factor activity / cellular response to amino acid starvation / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / ABC-family proteins mediated transport / PKR-mediated signaling / spindle / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / rRNA processing / cellular response to UV / protein tag activity / ribosomal small subunit biogenesis / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / virus receptor activity / cellular response to oxidative stress / cellular response to heat / small ribosomal subunit / T cell differentiation in thymus / cell body / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / tRNA binding / mitochondrial inner membrane / cell differentiation / postsynaptic density / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of apoptotic process Similarity search - Function | ||||||||||||
Biological species | rabbit (rabbit) / Hepatitis C virus (isolate 1) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Brown ZP / Abaeva IS / De S / Hellen CUT / Pestova TV / Frank J | ||||||||||||
Funding support | United States, 3 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_25539.map.gz | 228.1 MB | EMDB map data format | |
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Header (meta data) | emd-25539-v30.xml emd-25539.xml | 60.6 KB 60.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25539_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_25539.png | 38.8 KB | ||
Masks | emd_25539_msk_1.map | 244.1 MB | Mask map | |
Others | emd_25539_additional_1.map.gz emd_25539_additional_2.map.gz emd_25539_additional_3.map.gz emd_25539_half_map_1.map.gz emd_25539_half_map_2.map.gz | 122.4 MB 143.5 MB 192.2 MB 193.6 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25539 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25539 | HTTPS FTP |
-Validation report
Summary document | emd_25539_validation.pdf.gz | 977.6 KB | Display | EMDB validaton report |
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Full document | emd_25539_full_validation.pdf.gz | 977.2 KB | Display | |
Data in XML | emd_25539_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_25539_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25539 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25539 | HTTPS FTP |
-Related structure data
Related structure data | 7sysMC 7syiC 7syjC 7sykC 7sylC 7syoC 7sypC 7syqC 7syrC 7sytC 7syuC 7syvC 7sywC 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_25539.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 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_25539_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: Local resolution values
File | emd_25539_additional_1.map | ||||||||||||
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Annotation | Local resolution values | ||||||||||||
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-Additional map: Local resolution map filtered at local resolution
File | emd_25539_additional_2.map | ||||||||||||
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Annotation | Local resolution map filtered at local resolution | ||||||||||||
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Density Histograms |
-Additional map: Unsharpened map
File | emd_25539_additional_3.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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Density Histograms |
-Half map: Half map
File | emd_25539_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_25539_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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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 #38: HCV IRES
+Macromolecule #39: Met-tRNA-i-Met
+Macromolecule #2: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #3: uS2 (SA)
+Macromolecule #4: eS1
+Macromolecule #5: uS5
+Macromolecule #6: uS3
+Macromolecule #7: eS4 (S4 X isoform)
+Macromolecule #8: uS7
+Macromolecule #9: eS6
+Macromolecule #10: eS7
+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: eS21
+Macromolecule #25: uS8
+Macromolecule #26: uS12
+Macromolecule #27: eS24
+Macromolecule #28: eS25
+Macromolecule #29: eS26
+Macromolecule #30: eS27
+Macromolecule #31: eS28
+Macromolecule #32: uS14
+Macromolecule #33: eS30
+Macromolecule #34: eS31
+Macromolecule #35: Receptor for Activated C Kinase 1 (RACK1)
+Macromolecule #36: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #37: eL41
+Macromolecule #40: ZINC 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 - 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: 56000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |