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Yorodumi- EMDB-10775: Structure of a human 48S translational initiation complex - 40S body -
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Open data
- Basic information
Basic information
| Entry | Database: EMDB / ID: EMD-10775 | ||||||||||||
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| Title | Structure of a human 48S translational initiation complex - 40S body | ||||||||||||
|  Map data | |||||||||||||
|  Sample | 
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|  Keywords | eIF3 / ribosome / translation / initiation complex | ||||||||||||
| Function / homology |  Function and homology information positive regulation of mRNA binding / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / negative regulation of RNA splicing / neural crest cell differentiation / regulation of translational initiation ...positive regulation of mRNA binding / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / negative regulation of RNA splicing / neural crest cell differentiation / regulation of translational initiation / positive regulation of ubiquitin-protein transferase activity / 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 / TOR signaling / Protein hydroxylation / SARS-CoV-1 modulates host translation machinery / cellular response to ethanol / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ribosomal small subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Protein methylation / Nuclear events stimulated by ALK signaling in cancer / laminin binding / rough endoplasmic reticulum / 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 / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / erythrocyte differentiation / mRNA 3'-UTR binding / innate immune response in mucosa / maturation of SSU-rRNA / neural tube closure / small-subunit processome / translational initiation / RHO GTPases Activate Formins / response to insulin / GABA-ergic synapse / maintenance of translational fidelity / modification-dependent protein catabolic process / mRNA 5'-UTR binding / response to virus / Regulation of expression of SLITs and ROBOs / protein tag activity / RMTs methylate histone arginines / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / Separation of Sister Chromatids / antibacterial humoral response / glucose homeostasis / presynapse / ribosome binding / cell body / virus receptor activity / 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 / defense response to Gram-positive bacterium 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
Structure visualization
| Movie | 
 
 
  Movie viewer | 
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| Structure viewer | EM map:  SurfView  Molmil  Jmol/JSmol | 
| Supplemental images | 
- Downloads & links
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 | 
-Validation report
| Summary document |  emd_10775_validation.pdf.gz | 753.4 KB | Display |  EMDB validaton report | 
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| Full document |  emd_10775_full_validation.pdf.gz | 753 KB | Display | |
| Data in XML |  emd_10775_validation.xml.gz | 25.6 KB | Display | |
| Data in CIF |  emd_10775_validation.cif.gz | 34.3 KB | Display | |
| Arichive directory |  https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10775  ftp://ftp.pdbj.org/pub/emdb/validation_reports/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 ( | 
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| Similar structure data | 
- Links
Links
| EMDB pages |  EMDB (EBI/PDBe) /  EMDataResource | 
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| Related items in Molecule of the Month | 
- Map
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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| 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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| 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
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
Sample preparation
| Buffer | pH: 7.4 | 
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| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % | 
- Electron microscopy
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:  FIELD EMISSION GUN | 
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD | 
| Experimental equipment |  Model: Titan Krios / Image courtesy: FEI Company | 
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 Escherichia coli (E. coli)
Escherichia coli (E. coli)
