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Yorodumi- EMDB-19128: Structure of human eIF3 core from closed 48S translation initiati... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19128 | |||||||||
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Title | Structure of human eIF3 core from closed 48S translation initiation complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RIBOSOME / TRANSLATION / initiation / 48S / eIF / human / eukaryotic / factor / codon / scanning / open / reading | |||||||||
Function / homology | Function and homology information positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex ...positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / mRNA cap binding / eukaryotic 48S preinitiation complex / negative regulation of RNA splicing / metal-dependent deubiquitinase activity / regulation of translational initiation / 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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / 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 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytosolic ribosome / Mitotic Prometaphase / laminin binding / EML4 and NUDC in mitotic spindle formation / negative regulation of translational initiation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / translation initiation factor binding / Resolution of Sister Chromatid Cohesion / translation initiation factor activity / 90S preribosome / erythrocyte differentiation / maturation of SSU-rRNA / small-subunit processome / positive regulation of translation / translational initiation / RHO GTPases Activate Formins / PML body / negative regulation of ERK1 and ERK2 cascade / receptor tyrosine kinase binding / fibrillar center / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / rRNA processing / Separation of Sister Chromatids / metallopeptidase activity / ribosome biogenesis / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / SARS-CoV-2 modulates host translation machinery / cytosolic small ribosomal subunit / ubiquitinyl hydrolase 1 / microtubule / cysteine-type deubiquitinase activity / cytoplasmic translation / postsynaptic density / cell differentiation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / cadherin binding / translation / focal adhesion / mRNA binding / synapse / chromatin / nucleolus / negative regulation of apoptotic process / structural molecule activity / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / proteolysis / DNA binding / RNA binding / zinc ion binding / extracellular exosome / nucleoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Petrychenko V / Yi S-H / Liedtke D / Peng BZ / Rodnina MV / Fischer N | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2024 Title: Structural basis for translational control by the human 48S initiation complex from codon scanning toward subunit joining Authors: Petrychenko V / Yi S-H / Liedtke D / Peng BZ / Rodnina MV / Fischer N | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19128.map.gz | 47.8 MB | EMDB map data format | |
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Header (meta data) | emd-19128-v30.xml emd-19128.xml | 47.9 KB 47.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19128_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_19128.png | 206.8 KB | ||
Masks | emd_19128_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-19128.cif.gz | 12.8 KB | ||
Others | emd_19128_additional_1.map.gz emd_19128_additional_2.map.gz emd_19128_half_map_1.map.gz emd_19128_half_map_2.map.gz | 49.4 MB 40.6 MB 40.7 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19128 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19128 | HTTPS FTP |
-Related structure data
Related structure data | 8rg0MC 17696 17697 17698 17699 17700 17701 8pj1C 8pj2C 8pj3C 8pj4C 8pj5C 8pj6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19128.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19128_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human 48S initiation complex 40S-eIF1-eIF1A-eIF2-eIF3-tRNA-Met-mRNA
+Supramolecule #1: Human 48S initiation complex 40S-eIF1-eIF1A-eIF2-eIF3-tRNA-Met-mRNA
+Supramolecule #2: Human 48S initiation complex 40S-eIF1-eIF1A-eIF2-eIF3-tRNA-Met
+Supramolecule #3: mRNA
+Macromolecule #1: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #2: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #3: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #4: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #6: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #8: 40S ribosomal protein S27
+Macromolecule #9: 40S ribosomal protein S13
+Macromolecule #10: 40S ribosomal protein S17
+Macromolecule #11: 40S ribosomal protein SA
+Macromolecule #12: 40S ribosomal protein S3a
+Macromolecule #13: 40S ribosomal protein S14
+Macromolecule #14: 40S ribosomal protein S26
+Macromolecule #15: 40S ribosomal protein S28
+Macromolecule #16: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #17: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #18: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #19: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #5: mRNA
+Macromolecule #7: 18S rRNA
+Macromolecule #20: MAGNESIUM ION
+Macromolecule #21: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Manual blotting & plunge-freezing. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Electron-optical aberrations were corrected using a CETCOR Cs-corrector (CEOS, Heidelberg) aligned with the CETCORPLUS 4.6.9 software package (CEOS, Heidelberg). |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.5 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-8rg0: |