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Yorodumi- EMDB-26067: CryoEM structure of the human 40S small ribosomal subunit in comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26067 | ||||||||||||
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Title | CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B. | ||||||||||||
Map data | Sharpened map | ||||||||||||
Sample |
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Function / homology | Function and homology information protein-synthesizing GTPase / 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 / 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 ...protein-synthesizing GTPase / 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 / 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 / : / 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 / 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 / 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 / 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 / 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 / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / gastrulation / 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) / rough endoplasmic reticulum / spindle assembly / regulation of translational fidelity / MDM2/MDM4 family protein binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / negative regulation of smoothened signaling pathway / rescue of stalled ribosome / signaling adaptor activity / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / stress granule assembly / translation initiation factor binding / maturation of SSU-rRNA / positive regulation of intrinsic apoptotic signaling pathway / Mitotic Prometaphase / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / EML4 and NUDC in mitotic spindle formation / positive regulation of apoptotic signaling pathway / Maturation of protein E / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of microtubule polymerization Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Lapointe CP / Grosely R / Sokabe M / Alvarado C / Wang J / Montabana E / Villa N / Shin B / Dever T / Fraser C ...Lapointe CP / Grosely R / Sokabe M / Alvarado C / Wang J / Montabana E / Villa N / Shin B / Dever T / Fraser C / Fernandez IS / Puglisi JD | ||||||||||||
Funding support | United States, Sweden, 3 items
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Citation | Journal: Nature / Year: 2022 Title: eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining. Authors: Christopher P Lapointe / Rosslyn Grosely / Masaaki Sokabe / Carlos Alvarado / Jinfan Wang / Elizabeth Montabana / Nancy Villa / Byung-Sik Shin / Thomas E Dever / Christopher S Fraser / ...Authors: Christopher P Lapointe / Rosslyn Grosely / Masaaki Sokabe / Carlos Alvarado / Jinfan Wang / Elizabeth Montabana / Nancy Villa / Byung-Sik Shin / Thomas E Dever / Christopher S Fraser / Israel S Fernández / Joseph D Puglisi / Abstract: Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases. A key commitment step is when the ribosomal subunits join at a ...Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases. A key commitment step is when the ribosomal subunits join at a translation start site on a messenger RNA to form a functional ribosome. Here, we combined single-molecule spectroscopy and structural methods using an in vitro reconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when the universally conserved eukaryotic initiation factors eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we visualized initiation complexes that contained both eIF1A and eIF5B using single-particle cryo-electron microscopy. The resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the initiation complex to orient the initiator aminoacyl-tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during translation initiation in humans. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26067.map.gz | 381.3 MB | EMDB map data format | |
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Header (meta data) | emd-26067-v30.xml emd-26067.xml | 58.1 KB 58.1 KB | Display Display | EMDB header |
Images | emd_26067.png | 98.3 KB | ||
Masks | emd_26067_msk_1.map | 421.9 MB | Mask map | |
Others | emd_26067_additional_1.map.gz emd_26067_half_map_1.map.gz emd_26067_half_map_2.map.gz | 370.1 MB 375.2 MB 369.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26067 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26067 | HTTPS FTP |
-Related structure data
Related structure data | 7tqlMC 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_26067.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26067_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_26067_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_26067_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_26067_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human 40S ribosomal subunit in complex with eIF1A and eIF5B
+Supramolecule #1: human 40S ribosomal subunit in complex with eIF1A and eIF5B
+Macromolecule #1: Eukaryotic translation initiation factor 5B
+Macromolecule #4: Translation initiation factor eIF1A
+Macromolecule #5: ribosomal protein uS2
+Macromolecule #6: 40S ribosomal protein S2
+Macromolecule #7: 40S ribosomal protein S4, X isoform
+Macromolecule #8: 40S ribosomal protein S3
+Macromolecule #9: 40S ribosomal protein S6
+Macromolecule #10: 40S ribosomal protein S7
+Macromolecule #11: 40S ribosomal protein S8
+Macromolecule #12: 40S ribosomal protein S9
+Macromolecule #13: 40S ribosomal protein S5
+Macromolecule #14: 40S ribosomal protein S11
+Macromolecule #15: 40S ribosomal protein S10
+Macromolecule #16: ribosomal protein uS15
+Macromolecule #17: ribosomal protein eS12
+Macromolecule #18: ribosomal protein uS11
+Macromolecule #19: 40S ribosomal protein S15
+Macromolecule #20: 40S ribosomal protein S16
+Macromolecule #21: ribosomal protein eS17
+Macromolecule #22: ribosomal protein uS13
+Macromolecule #23: 40S ribosomal protein S19
+Macromolecule #24: ribosomal protein uS10
+Macromolecule #25: 40S ribosomal protein S15a
+Macromolecule #26: 40S ribosomal protein S23
+Macromolecule #27: Isoform 3 of 40S ribosomal protein S24
+Macromolecule #28: 40S ribosomal protein S21
+Macromolecule #29: ribosomal protein eS25
+Macromolecule #30: 40S ribosomal protein S27
+Macromolecule #31: 40S ribosomal protein S26
+Macromolecule #32: ribosomal protein eS28
+Macromolecule #33: ribosomal protein eS30
+Macromolecule #34: ribosomal protein uS14
+Macromolecule #35: 40S ribosomal protein S27a
+Macromolecule #36: ribosomal protein eL41
+Macromolecule #37: Receptor of activated protein C kinase 1
+Macromolecule #2: 18S ribosomal RNA
+Macromolecule #3: Human Met-tRNAiMet
+Macromolecule #38: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #39: GUANOSINE-5'-MONOPHOSPHATE
+Macromolecule #40: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 190000 |