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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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Keywords | ribosome biogenesis / 40S ribosome / RIBOSOME | |||||||||
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 / Methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...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 / Methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein methyltransferase activity / positive regulation of rRNA processing / tRNA methylation / 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 / U3 snoRNA binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / Translation initiation complex formation / mammalian oogenesis stage / activation-induced cell death of T cells / Protein hydroxylation / 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 / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of ubiquitin-dependent protein catabolic process / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / positive regulation of cell cycle / cytosolic ribosome / stress granule assembly / Mitotic Prometaphase / rough endoplasmic reticulum / EML4 and NUDC in mitotic spindle formation / gastrulation / transcription initiation-coupled chromatin remodeling / translation initiation factor binding / Resolution of Sister Chromatid Cohesion / 90S preribosome / Transferases; Transferring one-carbon groups; Methyltransferases / erythrocyte differentiation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / innate immune response in mucosa / translational initiation / methyltransferase activity / maturation of SSU-rRNA / neural tube closure / mRNA 3'-UTR binding / positive regulation of translation / RHO GTPases Activate Formins / small-subunit processome / maintenance of translational fidelity / response to virus / placenta development / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / rRNA processing / Separation of Sister Chromatids / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / chromatin organization / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / antibacterial humoral response / cell body / T cell differentiation in thymus / SARS-CoV-2 modulates host translation machinery / nuclear membrane / cytosolic small ribosomal subunit / cytoplasmic translation / postsynaptic density / cell differentiation / protein stabilization / rRNA binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (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 | 35.4 KB 35.4 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 | ||
Filedesc metadata | emd-32799.cif.gz | 10.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32799 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32799 | HTTPS FTP |
-Validation report
Summary document | emd_32799_validation.pdf.gz | 455 KB | Display | EMDB validaton report |
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Full document | emd_32799_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | emd_32799_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_32799_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32799 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |