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Yorodumi- EMDB-8190: m48S late-stage initiation complex, purified from rabbit reticulo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8190 | |||||||||
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Title | m48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eIF2 ternary complex and eIF3 i and g subunits relocated to the intersubunit face | |||||||||
Map data | None | |||||||||
Sample |
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Function / homology | Function and homology information viral translational termination-reinitiation / eukaryotic translation initiation factor 2 complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / protein-synthesizing GTPase / 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 ...viral translational termination-reinitiation / eukaryotic translation initiation factor 2 complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / protein-synthesizing GTPase / 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 / 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 / regulation of translational fidelity / 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 / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 stress granule / 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 / cytosolic large ribosomal subunit / 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 / DNA binding Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
Authors | Simonetti A / Brito Querido J / Myasnikov AG / Mancera-Martinez E / Renaud A / Kuhn L / Hashem Y | |||||||||
Citation | Journal: Mol Cell / Year: 2016 Title: eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition. Authors: Angelita Simonetti / Jailson Brito Querido / Alexander G Myasnikov / Eder Mancera-Martinez / Adeline Renaud / Lauriane Kuhn / Yaser Hashem / Abstract: mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal ...mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal 40S subunit, mRNA scanning for start codon, and accommodation of initiator tRNA at the 40S P site. eIF3, composed of 13 subunits, 8 core (a, c, e, f, h, l, k, and m) and 5 peripheral (b, d, g, i, and j), plays a central role during this process. Here we report a cryo-electron microscopy structure of a mammalian 48S initiation complex at 5.8 Å resolution. It shows the relocation of subunits eIF3i and eIF3g to the 40S intersubunit face on the GTPase binding site, at a late stage in initiation. On the basis of a previous study, we demonstrate the relocation of eIF3b to the 40S intersubunit face, binding below the eIF2-Met-tRNAi(Met) ternary complex upon mRNA attachment. Our analysis reveals the deep rearrangement of eIF3 and unravels the molecular mechanism underlying eIF3 function in mRNA scanning and timing of ribosomal subunit joining. | |||||||||
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_8190.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-8190-v30.xml emd-8190.xml | 58.8 KB 58.8 KB | Display Display | EMDB header |
Images | emd_8190.png | 54.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8190 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8190 | HTTPS FTP |
-Validation report
Summary document | emd_8190_validation.pdf.gz | 309.1 KB | Display | EMDB validaton report |
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Full document | emd_8190_full_validation.pdf.gz | 308.3 KB | Display | |
Data in XML | emd_8190_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8190 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8190 | HTTPS FTP |
-Related structure data
Related structure data | 5k0yMC 8195C 5k1hC M: atomic model generated by this map C: citing same article (ref.) |
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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_8190.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 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 : m48S late-stage initiation complex, purified from rabbit reticulo...
+Supramolecule #1: m48S late-stage initiation complex, purified from rabbit reticulo...
+Macromolecule #1: tRNA
+Macromolecule #2: 18S ribosomal RNA
+Macromolecule #3: mRNA
+Macromolecule #4: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #5: ribosomal protein uS17
+Macromolecule #6: ribosomal protein uS9
+Macromolecule #7: 40S ribosomal protein S4
+Macromolecule #8: ribosomal protein uS14
+Macromolecule #9: Ribosomal protein S9 (Predicted)
+Macromolecule #10: ribosomal protein uS13
+Macromolecule #11: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #12: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #13: ribosomal protein uS12
+Macromolecule #14: ribosomal protein eS19
+Macromolecule #15: eukaryotic initiation factor 2 Gamma subunit (eIF2-Gamma)
+Macromolecule #16: Eukaryotic translation initiation factor 3 subunit I
+Macromolecule #17: ribosomal protein uS7
+Macromolecule #18: ribosomal protein eS30
+Macromolecule #19: ribosomal protein eS25
+Macromolecule #20: ribosomal protein eS7
+Macromolecule #21: 40S ribosomal protein S27
+Macromolecule #22: ribosomal protein uS15
+Macromolecule #23: ribosomal protein uS8
+Macromolecule #24: 40S ribosomal protein S21
+Macromolecule #25: ribosomal protein uS5
+Macromolecule #26: eukaryotic initiation factor 2 subunit Beta (eIF2-Beta)
+Macromolecule #27: ribosomal protein eS17
+Macromolecule #28: ribosomal protein uS2
+Macromolecule #29: ribosomal protein uS3
+Macromolecule #30: ribosomal protein uS10
+Macromolecule #31: ribosomal protein eS1
+Macromolecule #32: ribosomal protein uS11
+Macromolecule #33: ribosomal protein eS26
+Macromolecule #34: ribosomal protein eS28
+Macromolecule #35: ribosomal protein RACK1
+Macromolecule #36: ribosomal protein uS19
+Macromolecule #37: 40S ribosomal protein S8
+Macromolecule #38: ribosomal protein eS31
+Macromolecule #39: 40S ribosomal protein S6
+Macromolecule #40: 40S ribosomal protein S12
+Macromolecule #41: 40S ribosomal protein S24
+Macromolecule #42: ribosomal protein eS10
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.6 |
Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-8 / Number grids imaged: 1 / Number real images: 5700 / Average exposure time: 1.5 sec. / Average electron dose: 24.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |