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- EMDB-10775: Structure of a human 48S translational initiation complex - 40S body -
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Open data
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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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![]() | eIF3 / ribosome / translation / initiation complex | ||||||||||||
Function / homology | ![]() positive regulation of mRNA binding / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / negative regulation of RNA splicing / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neural crest cell differentiation ...positive regulation of mRNA binding / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / negative regulation of RNA splicing / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neural crest cell differentiation / positive regulation of ubiquitin-protein transferase activity / regulation of translational initiation / negative regulation of bicellular tight junction assembly / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / fibroblast growth factor binding / Protein hydroxylation / TOR signaling / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / cellular response to ethanol / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit binding / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / 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) / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nuclear events stimulated by ALK signaling in cancer / rough endoplasmic reticulum / laminin binding / translation regulator activity / positive regulation of cell cycle / translation initiation factor binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / translation initiation factor activity / antiviral innate immune response / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cytosolic ribosome / stress granule assembly / Resolution of Sister Chromatid Cohesion / positive regulation of translation / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / innate immune response in mucosa / erythrocyte differentiation / mRNA 3'-UTR binding / maturation of SSU-rRNA / neural tube closure / small-subunit processome / translational initiation / modification-dependent protein catabolic process / RHO GTPases Activate Formins / protein tag activity / Regulation of expression of SLITs and ROBOs / response to insulin / GABA-ergic synapse / maintenance of translational fidelity / mRNA 5'-UTR binding / response to virus / RMTs methylate histone arginines / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / glucose homeostasis / presynapse / ribosome binding / virus receptor activity / cell body / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / SARS-CoV-2 modulates host translation machinery / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / tRNA binding / protein ubiquitination Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
![]() | Brito Querido J / Sokabe M | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 36.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 50.7 KB 50.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.7 KB | Display | ![]() |
Images | ![]() | 168.4 KB | ||
Filedesc metadata | ![]() | 11 KB | ||
Others | ![]() ![]() ![]() ![]() | 382 MB 391.4 MB 394 MB 393.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 753.4 KB | Display | ![]() |
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Full document | ![]() | 753 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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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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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
-Additional map: #1
File | emd_10775_additional_1.map | ||||||||||||
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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 |
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |