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Yorodumi- EMDB-32799: Cryo-EM structure of a human pre-40S ribosomal subunit - State UTP14 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32799 | |||||||||
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Title | Cryo-EM structure of a human pre-40S ribosomal subunit - State UTP14 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / peptidyl-glutamine methylation / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / tRNA modification in the nucleus and cytosol / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Methylation ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / peptidyl-glutamine methylation / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / tRNA modification in the nucleus and cytosol / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Methylation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / negative regulation of RNA splicing / neural crest cell differentiation / rRNA methylation / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / ubiquitin ligase inhibitor activity / U3 snoRNA binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / Translation initiation complex formation / Protein hydroxylation / TOR signaling / 90S preribosome / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / translation regulator activity / 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 / rough endoplasmic reticulum / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / positive regulation of cell cycle / translation initiation factor binding / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / translational initiation / transcription initiation-coupled chromatin remodeling / Resolution of Sister Chromatid Cohesion / Transferases; Transferring one-carbon groups; Methyltransferases / cytosolic ribosome / small-subunit processome / erythrocyte differentiation / positive regulation of translation / innate immune response in mucosa / mRNA 3'-UTR binding / neural tube closure / methyltransferase activity / RHO GTPases Activate Formins / maintenance of translational fidelity / response to virus / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / cytoplasmic ribonucleoprotein granule / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / Regulation of expression of SLITs and ROBOs / Separation of Sister Chromatids / cytosolic small ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / cell body / small ribosomal subunit / cytoplasmic translation / chromatin organization / antibacterial humoral response / SARS-CoV-2 modulates host translation machinery / nuclear membrane / postsynaptic density / cell differentiation / rRNA binding / protein stabilization / ribosome / structural constituent of ribosome / defense response to Gram-positive bacterium / ribonucleoprotein complex / translation / positive regulation of apoptotic process / protein heterodimerization activity / focal adhesion Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Cheng J / Lau B / Thoms M / Ameismeier M / Berninghausen O / Hurt E / Beckmann R | |||||||||
Funding support | 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: The nucleoplasmic phase of pre-40S formation prior to nuclear export. Authors: Jingdong Cheng / Benjamin Lau / Matthias Thoms / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann / Abstract: Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural ...Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32799.map.gz | 105.6 MB | EMDB map data format | |
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Header (meta data) | emd-32799-v30.xml emd-32799.xml | 33.6 KB 33.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32799_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_32799.png | 131.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32799 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32799 | HTTPS FTP |
-Related structure data
Related structure data | 7wtsMC 7wtnC 7wtoC 7wtpC 7wtqC 7wtrC 7wttC 7wtuC 7wtvC 7wtwC 7wtxC 7wtzC 7wu0C 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_32799.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Yeast pre-40S ribosomal subunit
+Supramolecule #1: Yeast pre-40S ribosomal subunit
+Macromolecule #1: 18S rRNA
+Macromolecule #2: 40S ribosomal protein S27
+Macromolecule #3: 40S ribosomal protein S3a
+Macromolecule #4: 40S ribosomal protein S4, X isoform
+Macromolecule #5: 40S ribosomal protein S30
+Macromolecule #6: 40S ribosomal protein S7
+Macromolecule #7: 40S ribosomal protein S6
+Macromolecule #8: 40S ribosomal protein S24
+Macromolecule #9: RNA-binding protein PNO1
+Macromolecule #10: 40S ribosomal protein S23
+Macromolecule #11: 40S ribosomal protein S15a
+Macromolecule #12: Pre-rRNA-processing protein TSR1 homolog
+Macromolecule #13: 40S ribosomal protein S14
+Macromolecule #14: 40S ribosomal protein S13
+Macromolecule #15: 40S ribosomal protein S11
+Macromolecule #16: 40S ribosomal protein S9
+Macromolecule #17: 40S ribosomal protein S8
+Macromolecule #18: Multifunctional methyltransferase subunit TRM112-like protein
+Macromolecule #19: Probable 18S rRNA (guanine-N(7))-methyltransferase
+Macromolecule #20: RRP12-like protein
+Macromolecule #21: Ribosome biogenesis protein SLX9 homolog
+Macromolecule #22: U3 small nucleolar RNA-associated protein 14 homolog A
+Macromolecule #23: Probable dimethyladenosine transferase
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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 | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |