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Yorodumi- EMDB-14114: Structure of the human 48S initiation complex in closed state (h4... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14114 | |||||||||
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Title | Structure of the human 48S initiation complex in closed state (h48S AUG closed) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 48S / initiation / eIF3 / ternary complex / translation / open state / RIBOSOME | |||||||||
Function / homology | Function and homology information positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / viral translational termination-reinitiation / glial limiting end-foot / response to kainic acid / eukaryotic translation initiation factor 3 complex, eIF3e / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / cap-dependent translational initiation ...positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / viral translational termination-reinitiation / glial limiting end-foot / response to kainic acid / eukaryotic translation initiation factor 3 complex, eIF3e / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / cap-dependent translational initiation / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of translational initiation in response to stress / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / eukaryotic translation initiation factor 2 complex / IRES-dependent viral translational initiation / PERK regulates gene expression / regulation of translational initiation in response to stress / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / translation factor activity, RNA binding / protein-synthesizing GTPase / mRNA cap binding / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / 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 / protein tyrosine kinase inhibitor activity / eukaryotic 48S preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / metal-dependent deubiquitinase activity / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / : / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / regulation of translational initiation / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / pigmentation / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / Protein hydroxylation / iron-sulfur cluster binding / TOR signaling / protein deubiquitination / BH3 domain binding / mTORC1-mediated signalling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / Selenocysteine synthesis / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Yi S-H / Petrychenko V / Schliep JE / Goyal A / Linden A / Chari A / Urlaub H / Stark H / Rodnina MV / Adio S / Fischer N | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: Conformational rearrangements upon start codon recognition in human 48S translation initiation complex. Authors: Sung-Hui Yi / Valentyn Petrychenko / Jan Erik Schliep / Akanksha Goyal / Andreas Linden / Ashwin Chari / Henning Urlaub / Holger Stark / Marina V Rodnina / Sarah Adio / Niels Fischer / Abstract: Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of ...Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of codon recognition by kinetic methods using eIF1A as a reporter. Both approaches capture two distinct ribosome populations formed on an mRNA with a cognate AUG codon in the presence of eIF1, eIF1A, eIF2-GTP-Met-tRNAiMet and eIF3. The 'open' 40S subunit conformation differs from the human 48S scanning complex and represents an intermediate preceding the codon recognition step. The 'closed' form is similar to reported structures of complexes from yeast and mammals formed upon codon recognition, except for the orientation of eIF1A, which is unique in our structure. Kinetic experiments show how various initiation factors mediate the population distribution of open and closed conformations until 60S subunit docking. Our results provide insights into the timing and structure of human translation initiation intermediates and suggest the differences in the mechanisms of start codon selection between mammals and yeast. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14114.map.gz | 159.6 MB | EMDB map data format | |
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Header (meta data) | emd-14114-v30.xml emd-14114.xml | 74.9 KB 74.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14114_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_14114.png | 115.2 KB | ||
Masks | emd_14114_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-14114.cif.gz | 18 KB | ||
Others | emd_14114_half_map_1.map.gz emd_14114_half_map_2.map.gz | 140.4 MB 140.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14114 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14114 | HTTPS FTP |
-Related structure data
Related structure data | 7qp7MC 7qp6C 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 |
EM raw data | EMPIAR-11005 (Title: Conformational rearrangements upon start codon recognition in human 48S translation initiation complex Data size: 1.1 TB Data #1: Motion-corrected, dose-weighted micrographs [micrographs - single frame] Data #2: Particles of human 48S IC in open state ("open") [picked particles - single frame - processed] Data #3: Particles of human 48S IC in closed state ("closed") [picked particles - single frame - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14114.map.gz / Format: CCP4 / Size: 178 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: 1.16 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14114_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14114_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14114_half_map_2.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
+Macromolecule #1: Eukaryotic translation initiation factor 3 subunit B
+Macromolecule #2: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #3: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #4: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #5: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #7: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #8: 60S ribosomal protein L41
+Macromolecule #10: 40S ribosomal protein S11
+Macromolecule #11: 40S ribosomal protein S4, X isoform
+Macromolecule #12: 40S ribosomal protein S9
+Macromolecule #13: 40S ribosomal protein S23
+Macromolecule #14: 40S ribosomal protein S30
+Macromolecule #15: 40S ribosomal protein S7
+Macromolecule #16: 40S ribosomal protein S27
+Macromolecule #17: 40S ribosomal protein S13
+Macromolecule #18: 40S ribosomal protein S15a
+Macromolecule #19: 40S ribosomal protein S21
+Macromolecule #20: 40S ribosomal protein S2
+Macromolecule #21: 40S ribosomal protein S17
+Macromolecule #22: 40S ribosomal protein SA
+Macromolecule #23: 40S ribosomal protein S3a
+Macromolecule #24: 40S ribosomal protein S14
+Macromolecule #25: 40S ribosomal protein S26
+Macromolecule #26: 40S ribosomal protein S8
+Macromolecule #27: 40S ribosomal protein S6
+Macromolecule #28: 40S ribosomal protein S24
+Macromolecule #29: 40S ribosomal protein S5
+Macromolecule #30: 40S ribosomal protein S16
+Macromolecule #31: 40S ribosomal protein S3
+Macromolecule #32: 40S ribosomal protein S10
+Macromolecule #33: 40S ribosomal protein S15
+Macromolecule #34: Receptor of activated protein C kinase 1
+Macromolecule #35: 40S ribosomal protein S19
+Macromolecule #36: 40S ribosomal protein S25
+Macromolecule #37: 40S ribosomal protein S18
+Macromolecule #38: 40S ribosomal protein S20
+Macromolecule #39: 40S ribosomal protein S29
+Macromolecule #40: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #41: 40S ribosomal protein S12
+Macromolecule #42: 40S ribosomal protein S28
+Macromolecule #43: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #44: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #45: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #46: Eukaryotic translation initiation factor 2 subunit 3
+Macromolecule #47: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #48: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #50: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #51: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #6: mRNA
+Macromolecule #9: 18S rRNA
+Macromolecule #49: Initiator Met-tRNA-i
+Macromolecule #52: 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 Details: 20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | Aberration corrections performed using Cs image corrector (CEOS company) |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 15544 / Average exposure time: 1.0 sec. / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |