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- EMDB-14113: Structure of the human 48S initiation complex in open state (h48S... -
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Open data
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Basic information
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Title | Structure of the human 48S initiation complex in open state (h48S AUG open) | |||||||||
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![]() | 48S / initiation / eIF3 / ternary complex / translation / open state / RIBOSOME | |||||||||
Function / homology | ![]() male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation / Cellular response to mitochondrial stress / positive regulation of mRNA cis splicing, via spliceosome / response to manganese-induced endoplasmic reticulum stress ...male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation / Cellular response to mitochondrial stress / positive regulation of mRNA cis splicing, via spliceosome / response to manganese-induced endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / translation reinitiation / PERK-mediated unfolded protein response / IRES-dependent viral translational initiation / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / regulation of translational initiation in response to stress / multi-eIF complex / eukaryotic translation initiation factor 3 complex / selenocysteine metabolic process / selenocysteine incorporation / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation 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 / eukaryotic 48S preinitiation complex / response to TNF agonist / positive regulation of base-excision repair / 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 RNA splicing / negative regulation of DNA repair / metal-dependent deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of translational initiation / regulation of establishment of cell polarity / negative regulation of phagocytosis / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / protein kinase A binding / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / pigmentation / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / protein deubiquitination / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / monocyte chemotaxis / Selenocysteine synthesis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity Similarity search - 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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
![]() | 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 | ![]()
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![]() | ![]() 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 | ![]() | 162.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 77.4 KB 77.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 119.2 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 18.3 KB | ||
Others | ![]() ![]() | 140.7 MB 140.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 956.9 KB | Display | ![]() |
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Full document | ![]() | 956.5 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qp6MC ![]() 7qp7C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() 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]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
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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 1
+Macromolecule #45: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #46: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #47: Eukaryotic translation initiation factor 2 subunit 2
+Macromolecule #48: Eukaryotic translation initiation factor 2 subunit 3
+Macromolecule #49: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #50: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #52: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #53: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #6: mRNA
+Macromolecule #9: 18S rRNA
+Macromolecule #51: Initiator Met-tRNA-i
+Macromolecule #54: ZINC ION
+Macromolecule #55: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |