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Yorodumi- EMDB-10769: Structure of a human 48S translational initiation complex - eIF3 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10769 | ||||||||||||
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Title | Structure of a human 48S translational initiation complex - eIF3 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | eIF3 / ribosome / translation / initiation complex | ||||||||||||
Function / homology | Function and homology information positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex ...positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / mRNA cap binding / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / negative regulation of RNA splicing / metal-dependent deubiquitinase activity / neural crest cell differentiation / regulation of translational initiation / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / fibroblast growth factor binding / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / translation regulator activity / laminin binding / rough endoplasmic reticulum / Mitotic Prometaphase / antiviral innate immune response / EML4 and NUDC in mitotic spindle formation / 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) / negative regulation of translational initiation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / translation initiation factor binding / cytosolic ribosome / Resolution of Sister Chromatid Cohesion / translation initiation factor activity / erythrocyte differentiation / maturation of SSU-rRNA / positive regulation of translation / neural tube closure / small-subunit processome / mRNA 3'-UTR binding / translational initiation / RHO GTPases Activate Formins / PML body / fibrillar center / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / mRNA 5'-UTR binding / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / Separation of Sister Chromatids / rRNA processing / metallopeptidase activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal small subunit assembly / virus receptor activity / small ribosomal subunit / cytosolic small ribosomal subunit / SARS-CoV-2 modulates host translation machinery / cytoplasmic translation / microtubule / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cell differentiation / postsynaptic density / protein stabilization / ribosome / structural constituent of ribosome / cadherin binding / ribonucleoprotein complex / translation / focal adhesion / mRNA binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Brito Querido J / Sokabe M | ||||||||||||
Funding support | United Kingdom, United States, 3 items
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Citation | Journal: Science / Year: 2020 Title: Structure of a human 48 translational initiation complex. Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan / Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning. | ||||||||||||
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_10769.map.gz | 11.4 MB | EMDB map data format | |
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Header (meta data) | emd-10769-v30.xml emd-10769.xml | 37.9 KB 37.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10769_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_10769.png | 56 KB | ||
Masks | emd_10769_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-10769.cif.gz | 10 KB | ||
Others | emd_10769_additional.map.gz emd_10769_half_map_1.map.gz emd_10769_half_map_2.map.gz | 64.3 MB 64.6 MB 64.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10769 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10769 | HTTPS FTP |
-Validation report
Summary document | emd_10769_validation.pdf.gz | 422.2 KB | Display | EMDB validaton report |
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Full document | emd_10769_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | emd_10769_validation.xml.gz | 18.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10769 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10769 | HTTPS FTP |
-Related structure data
Related structure data | 6ybdMC 6ybsC 6ybtC 6ybvC 6ybwC 6zmwC 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_10769.map.gz / Format: CCP4 / Size: 83.7 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: 1.074 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10769_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_10769_additional.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_10769_half_map_1.map | ||||||||||||
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-Half map: #2
File | emd_10769_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : 48S initiation complex
+Supramolecule #1: 48S initiation complex
+Macromolecule #1: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #2: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #3: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #4: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #5: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #6: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #7: 40S ribosomal protein S7
+Macromolecule #8: 40S ribosomal protein S27
+Macromolecule #9: 40S ribosomal protein S21
+Macromolecule #10: 40S ribosomal protein S17
+Macromolecule #11: 40S ribosomal protein S2
+Macromolecule #12: 40S ribosomal protein S3a
+Macromolecule #13: 40S ribosomal protein SA
+Macromolecule #14: 40S ribosomal protein S26
+Macromolecule #15: 40S ribosomal protein S14
+Macromolecule #16: 40S ribosomal protein S13
+Macromolecule #17: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #18: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #19: Eukaryotic translation initiation factor 3 subunit L
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 107.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |