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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 | ||||||||||||
Map data | |||||||||||||
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 / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / eukaryotic 48S preinitiation complex / negative regulation of RNA splicing / neural crest cell differentiation ...positive regulation of mRNA binding / positive regulation of mRNA cis splicing, via spliceosome / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 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 / 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 / mammalian oogenesis stage / activation-induced cell death of T cells / fibroblast growth factor binding / Protein hydroxylation / mTORC1-mediated signalling / 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 / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / ribosomal small subunit binding / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 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 / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Protein methylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / translation regulator activity / Nuclear events stimulated by ALK signaling in cancer / positive regulation of cell cycle / stress granule assembly / Mitotic Prometaphase / cytosolic ribosome / laminin binding / 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) / rough endoplasmic reticulum / antiviral innate immune response / gastrulation / translation initiation factor binding / Resolution of Sister Chromatid Cohesion / translation initiation factor activity / ribosome assembly / erythrocyte differentiation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / innate immune response in mucosa / maturation of SSU-rRNA / neural tube closure / placenta development / small-subunit processome / mRNA 3'-UTR binding / positive regulation of translation / translational initiation / RHO GTPases Activate Formins / maintenance of translational fidelity / response to virus / G1/S transition of mitotic cell cycle / RMTs methylate histone arginines / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / Separation of Sister Chromatids / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / virus receptor activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / antibacterial humoral response / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / SARS-CoV-2 modulates host translation machinery / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation 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 |
-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 (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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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 |