[English] 日本語
Yorodumi- EMDB-17701: Structure of human 48S translation initiation complex with initia... -
+
Open data
-
Basic information
| Entry | ![]() | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Title | Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and eIF3 (off-pathway) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | RIBOSOME / TRANSLATION / initiation / 48S / eIF / human / eukaryotic / factor / codon / scanning / closed | |||||||||
| Function / homology | Function and homology informationpositive 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 / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / cytoplasmic translational initiation ...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 / IRES-dependent viral translational initiation / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / cytoplasmic translational initiation / multi-eIF complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / mRNA cap binding / eukaryotic 48S preinitiation complex / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / IRE1-RACK1-PP2A complex / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / metal-dependent deubiquitinase activity / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cysteine-type endopeptidase activator activity involved in apoptotic process / regulation of translational initiation / oxidized purine DNA binding / positive regulation of ubiquitin-protein transferase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / 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 / protein kinase A binding / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / monocyte chemotaxis / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / TOR signaling / Protein hydroxylation / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / iron-sulfur cluster binding / regulation of cell division / 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 / 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 / positive regulation of GTPase activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / protein serine/threonine kinase inhibitor activity / positive regulation of signal transduction by p53 class mediator / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / 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 / phagocytic cup / regulation of translational fidelity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of protein binding / 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 / Nuclear events stimulated by ALK signaling in cancer / positive regulation of intrinsic apoptotic signaling pathway / spindle assembly / laminin binding Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Petrychenko V / Yi S-H / Liedtke D / Peng BZ / Rodnina MV / Fischer N | |||||||||
| Funding support | Germany, 2 items
| |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2025Title: Structural basis for translational control by the human 48S initiation complex. Authors: Valentyn Petrychenko / Sung-Hui Yi / David Liedtke / Bee-Zen Peng / Marina V Rodnina / Niels Fischer / ![]() Abstract: The selection of an open reading frame (ORF) for translation of eukaryotic mRNA relies on remodeling of the scanning 48S initiation complex into an elongation-ready 80S ribosome. Using cryo-electron ...The selection of an open reading frame (ORF) for translation of eukaryotic mRNA relies on remodeling of the scanning 48S initiation complex into an elongation-ready 80S ribosome. Using cryo-electron microscopy, we visualize the key commitment steps orchestrating 48S remodeling in humans. The mRNA Kozak sequence facilitates mRNA scanning in the 48S open state and stabilizes the 48S closed state by organizing the contacts of eukaryotic initiation factors (eIFs) and ribosomal proteins and by reconfiguring mRNA structure. GTPase-triggered large-scale fluctuations of 48S-bound eIF2 facilitate eIF5B recruitment, transfer of initiator tRNA from eIF2 to eIF5B and the release of eIF5 and eIF2. The 48S-bound multisubunit eIF3 complex controls ribosomal subunit joining by coupling eIF exchange to gradual displacement of the eIF3c N-terminal domain from the intersubunit interface. These findings reveal the structural mechanism of ORF selection in human cells and explain how eIF3 could function in the context of the 80S ribosome. | |||||||||
| History |
|
-
Structure visualization
| Supplemental images |
|---|
-
Downloads & links
-EMDB archive
| Map data | emd_17701.map.gz | 140.4 MB | EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) | emd-17701-v30.xml emd-17701.xml | 72.6 KB 72.6 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_17701_fsc.xml | 12.7 KB | Display | FSC data file |
| Images | emd_17701.png | 150.7 KB | ||
| Masks | emd_17701_msk_1.map | 178 MB | Mask map | |
| Filedesc metadata | emd-17701.cif.gz | 17.6 KB | ||
| Others | emd_17701_half_map_1.map.gz emd_17701_half_map_2.map.gz | 140.6 MB 140.7 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17701 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17701 | HTTPS FTP |
-Validation report
| Summary document | emd_17701_validation.pdf.gz | 987 KB | Display | EMDB validaton report |
|---|---|---|---|---|
| Full document | emd_17701_full_validation.pdf.gz | 986.6 KB | Display | |
| Data in XML | emd_17701_validation.xml.gz | 20.4 KB | Display | |
| Data in CIF | emd_17701_validation.cif.gz | 27 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17701 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17701 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8pj6MC ![]() 8pj1C ![]() 8pj2C ![]() 8pj3C ![]() 8pj4C ![]() 8pj5C ![]() 8rg0C M: atomic model generated by this map C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| Related items in Molecule of the Month |
-
Map
| File | Download / File: emd_17701.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
|
-Supplemental data
-Mask #1
| File | emd_17701_msk_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-Half map: #2
| File | emd_17701_half_map_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-Half map: #1
| File | emd_17701_half_map_2.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-
Sample components
+Entire : Human 48S initiation complex 40S-eIF1A-eIF3-tRNA-Met-mRNA
+Supramolecule #1: Human 48S initiation complex 40S-eIF1A-eIF3-tRNA-Met-mRNA
+Macromolecule #1: Eukaryotic translation initiation factor 3 subunit B
+Macromolecule #2: Eukaryotic translation initiation factor 3 subunit I
+Macromolecule #3: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #4: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #5: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #6: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #8: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #9: 60S ribosomal protein L41
+Macromolecule #11: 40S ribosomal protein S11
+Macromolecule #12: 40S ribosomal protein S4, X isoform
+Macromolecule #13: 40S ribosomal protein S9
+Macromolecule #14: 40S ribosomal protein S23
+Macromolecule #15: 40S ribosomal protein S30
+Macromolecule #16: 40S ribosomal protein S7
+Macromolecule #17: 40S ribosomal protein S27
+Macromolecule #18: 40S ribosomal protein S13
+Macromolecule #19: 40S ribosomal protein S15a
+Macromolecule #20: 40S ribosomal protein S21
+Macromolecule #21: 40S ribosomal protein S2
+Macromolecule #22: 40S ribosomal protein S17
+Macromolecule #23: 40S ribosomal protein SA
+Macromolecule #24: 40S ribosomal protein S3a
+Macromolecule #25: 40S ribosomal protein S14
+Macromolecule #26: 40S ribosomal protein S26
+Macromolecule #27: 40S ribosomal protein S8
+Macromolecule #28: 40S ribosomal protein S6
+Macromolecule #29: 40S ribosomal protein S24
+Macromolecule #30: 40S ribosomal protein S5
+Macromolecule #31: 40S ribosomal protein S16
+Macromolecule #32: 40S ribosomal protein S3
+Macromolecule #33: 40S ribosomal protein S10
+Macromolecule #34: 40S ribosomal protein S15
+Macromolecule #35: Receptor of activated protein C kinase 1
+Macromolecule #36: 40S ribosomal protein S19
+Macromolecule #37: 40S ribosomal protein S25
+Macromolecule #38: 40S ribosomal protein S18
+Macromolecule #39: 40S ribosomal protein S20
+Macromolecule #40: 40S ribosomal protein S29
+Macromolecule #41: Ubiquitin
+Macromolecule #42: 40S ribosomal protein S12
+Macromolecule #43: 40S ribosomal protein S28
+Macromolecule #44: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #45: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #46: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #47: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #49: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #50: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #7: mRNA
+Macromolecule #10: 18S rRNA
+Macromolecule #48: Initiator Met-tRNA-i
+Macromolecule #51: MAGNESIUM ION
+Macromolecule #52: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | particle |
-
Sample preparation
| Buffer | pH: 7.5 Component:
| ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Manual blotting & plunge-freezing. |
-
Electron microscopy
| Microscope | FEI TITAN KRIOS |
|---|---|
| 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) / 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 / 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 |
Movie
Controller
About Yorodumi



Keywords
Homo sapiens (human)
Authors
Germany, 2 items
Citation












































Z (Sec.)
Y (Row.)
X (Col.)













































Processing
FIELD EMISSION GUN

