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Yorodumi- EMDB-10775: Structure of a human 48S translational initiation complex - 40S body -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10775 | ||||||||||||
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Title | Structure of a human 48S translational initiation complex - 40S body | ||||||||||||
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Sample |
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Keywords | eIF3 / ribosome / translation / initiation complex | ||||||||||||
Function / homology | Function and homology information positive regulation of mRNA binding / positive regulation of mRNA cis splicing, via spliceosome / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / negative regulation of RNA splicing / laminin receptor activity ...positive regulation of mRNA binding / positive regulation of mRNA cis splicing, via spliceosome / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / negative regulation of RNA splicing / laminin receptor activity / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / regulation of translational initiation / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / ubiquitin ligase inhibitor 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 / Protein hydroxylation / TOR signaling / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / ribosomal small subunit binding / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / positive regulation of cell cycle / translation initiation factor binding / stress granule assembly / maturation of SSU-rRNA / Mitotic Prometaphase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / EML4 and NUDC in mitotic spindle formation / negative regulation of ubiquitin-dependent protein catabolic process / translational initiation / Resolution of Sister Chromatid Cohesion / ribosome assembly / translation initiation factor activity / small-subunit processome / cytosolic ribosome / erythrocyte differentiation / positive regulation of translation / innate immune response in mucosa / mRNA 3'-UTR binding / neural tube closure / RHO GTPases Activate Formins / maintenance of translational fidelity / response to virus / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / cytoplasmic ribonucleoprotein granule / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / RMTs methylate histone arginines / rRNA processing / Regulation of expression of SLITs and ROBOs / Separation of Sister Chromatids / cytosolic small ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / ribosome binding / glucose homeostasis / virus receptor activity / cell body / cytoplasmic translation / small ribosomal subunit / cytosolic large ribosomal subunit / antibacterial humoral response / SARS-CoV-2 modulates host translation machinery / tRNA binding / postsynaptic density / cell differentiation / rRNA binding / protein stabilization / ribosome / structural constituent of ribosome / defense response to Gram-positive bacterium / cadherin binding / ribonucleoprotein complex Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 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_10775.map.gz | 36.6 MB | EMDB map data format | |
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Header (meta data) | emd-10775-v30.xml emd-10775.xml | 50.7 KB 50.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10775_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_10775.png | 168.4 KB | ||
Filedesc metadata | emd-10775.cif.gz | 11 KB | ||
Others | emd_10775_additional_1.map.gz emd_10775_additional_2.map.gz emd_10775_half_map_1.map.gz emd_10775_half_map_2.map.gz | 382 MB 391.4 MB 394 MB 393.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10775 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10775 | HTTPS FTP |
-Related structure data
Related structure data | 6ybwMC 6ybdC 6ybsC 6ybtC 6ybvC 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_10775.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Additional map: #1
File | emd_10775_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_10775_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10775_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10775_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human 48S initiation complex
+Supramolecule #1: Human 48S initiation complex
+Supramolecule #2: Human 48S initiation complex
+Supramolecule #3: Human 48S initiation complex
+Supramolecule #4: Human 48S initiation complex
+Macromolecule #1: 40S ribosomal protein S4, X isoform
+Macromolecule #2: 40S ribosomal protein S11
+Macromolecule #3: 40S ribosomal protein S23
+Macromolecule #4: 40S ribosomal protein S9
+Macromolecule #5: 40S ribosomal protein S7
+Macromolecule #6: 40S ribosomal protein S30
+Macromolecule #7: 40S ribosomal protein S27
+Macromolecule #8: 40S ribosomal protein S21
+Macromolecule #9: 40S ribosomal protein S15a
+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 S6
+Macromolecule #17: 40S ribosomal protein S8
+Macromolecule #18: 40S ribosomal protein S24
+Macromolecule #19: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #20: Eukaryotic translation initiation factor 1
+Macromolecule #21: 40S ribosomal protein S13
+Macromolecule #22: Eukaryotic translation initiation factor 3 subunit J
+Macromolecule #23: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #24: 60S ribosomal protein L41
+Macromolecule #25: 18S rRNA
+Macromolecule #26: mRNA
+Macromolecule #27: MAGNESIUM ION
+Macromolecule #28: ZINC ION
-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 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 107.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |