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- EMDB-25539: Structure of the delta dII IRES eIF2-containing 48S initiation co... -
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Basic information
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Title | Structure of the delta dII IRES eIF2-containing 48S initiation complex, closed conformation. Structure 12(delta dII). | ||||||||||||
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Function / homology | ![]() regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / 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 ...regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / 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 / eukaryotic translation initiation factor 2 complex / regulation of translational initiation in response to stress / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / ribosomal subunit / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cytosolic ribosome / stress granule assembly / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / translational initiation / 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 / response to endoplasmic reticulum stress / 90S preribosome / 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 / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / placenta development / PKR-mediated signaling / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / cellular response to UV / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / glucose homeostasis / virus receptor activity / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cellular response to heat / small ribosomal subunit / small ribosomal subunit rRNA binding / cellular response to oxidative stress / cell body / T cell differentiation in thymus / perikaryon / cytosolic small ribosomal subunit / mitochondrial inner membrane / tRNA binding / cytoplasmic translation / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Brown ZP / Abaeva IS / De S / Hellen CUT / Pestova TV / Frank J | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 228.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 60.6 KB 60.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 38.8 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() ![]() | 122.4 MB 143.5 MB 192.2 MB 193.6 MB 193.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 977.6 KB | Display | ![]() |
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Full document | ![]() | 977.2 KB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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-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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-Additional map: Unsharpened map
File | emd_25539_additional_3.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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-Half map: Half map
File | emd_25539_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
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-Half map: Half map
File | emd_25539_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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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. |
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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: ![]() |
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 |