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Yorodumi- EMDB-10772: Structure of a human 48S translational initiation complex - head -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10772 | ||||||||||||
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Title | Structure of a human 48S translational initiation complex - head | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | ribosome / translation / initiation complex | ||||||||||||
Function / homology | Function and homology information positive regulation of mRNA binding / viral translational termination-reinitiation / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis ...positive regulation of mRNA binding / viral translational termination-reinitiation / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 48S preinitiation complex / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / protein kinase A binding / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / pigmentation / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division / monocyte chemotaxis / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / phagocytic cup / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / cyclin binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / positive regulation of DNA repair / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / ribosomal small subunit export from nucleus / signaling adaptor activity / negative regulation of smoothened signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / cytosolic ribosome / positive regulation of JUN kinase activity / Maturation of protein E / Maturation of protein E / gastrulation / ER Quality Control Compartment (ERQC) / MDM2/MDM4 family protein binding / Myoclonic epilepsy of Lafora / negative regulation of protein ubiquitination / enzyme activator activity / positive regulation of microtubule polymerization / FLT3 signaling by CBL mutants / DNA-(apurinic or apyrimidinic site) endonuclease activity / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins 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_10772.map.gz | 27.7 MB | EMDB map data format | |
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Header (meta data) | emd-10772-v30.xml emd-10772.xml | 37.6 KB 37.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10772_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_10772.png | 168.4 KB | ||
Masks | emd_10772_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-10772.cif.gz | 9.2 KB | ||
Others | emd_10772_additional_1.map.gz emd_10772_additional_2.map.gz emd_10772_half_map_1.map.gz emd_10772_half_map_2.map.gz | 382 MB 394.2 MB 394.6 MB 394.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10772 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10772 | HTTPS FTP |
-Validation report
Summary document | emd_10772_validation.pdf.gz | 629 KB | Display | EMDB validaton report |
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Full document | emd_10772_full_validation.pdf.gz | 628.6 KB | Display | |
Data in XML | emd_10772_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | emd_10772_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10772 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10772 | HTTPS FTP |
-Related structure data
Related structure data | 6ybsMC 6ybdC 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_10772.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
-Mask #1
File | emd_10772_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_10772_additional_1.map | ||||||||||||
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-Additional map: #2
File | emd_10772_additional_2.map | ||||||||||||
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-Half map: #1
File | emd_10772_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_10772_half_map_2.map | ||||||||||||
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Projections & Slices |
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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 D
+Macromolecule #2: Receptor of activated protein C kinase 1
+Macromolecule #3: 40S ribosomal protein S28
+Macromolecule #4: 40S ribosomal protein S17
+Macromolecule #5: 40S ribosomal protein S20
+Macromolecule #6: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #7: 40S ribosomal protein S10
+Macromolecule #8: 40S ribosomal protein S12
+Macromolecule #9: 40S ribosomal protein S29
+Macromolecule #10: 40S ribosomal protein S15
+Macromolecule #11: 40S ribosomal protein S3
+Macromolecule #12: 40S ribosomal protein S19
+Macromolecule #13: 40S ribosomal protein S25
+Macromolecule #14: 40S ribosomal protein S18
+Macromolecule #15: 40S ribosomal protein S5
+Macromolecule #16: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #17: 40S ribosomal protein S16
+Macromolecule #18: 18S rRNA
+Macromolecule #19: MAGNESIUM ION
+Macromolecule #20: 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 % / 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 |