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Yorodumi- EMDB-32800: Cryo-EM structure of a human pre-40S ribosomal subunit - State RR... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32800 | |||||||||
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Title | Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribosome biogenesis / 40S ribosome / RIBOSOME | |||||||||
Function / homology | Function and homology information peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / Activation of SMO / intermediate filament cytoskeleton organization / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA modification in the nucleus and cytosol / negative regulation of NLRP3 inflammasome complex assembly ...peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / Activation of SMO / intermediate filament cytoskeleton organization / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA modification in the nucleus and cytosol / negative regulation of NLRP3 inflammasome complex assembly / Methylation / trophectodermal cell differentiation / protein methyltransferase activity / positive regulation of rRNA processing / tRNA methylation / cellular response to nutrient / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / positive regulation of respiratory burst involved in inflammatory response / beta-catenin destruction complex / nucleolus organization / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / negative regulation of RNA splicing / rRNA methylation / U3 snoRNA binding / neural crest cell differentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / preribosome, small subunit precursor / negative regulation of ubiquitin protein ligase activity / positive regulation of Rho protein signal transduction / Ribosomal scanning and start codon recognition / snoRNA binding / Translation initiation complex formation / fibroblast growth factor binding / mammalian oogenesis stage / activation-induced cell death of T cells / monocyte chemotaxis / Golgi organization / 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 / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / negative regulation of respiratory burst involved in inflammatory response / 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 / 90S preribosome / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / T cell proliferation involved in immune response / positive regulation of cell cycle / regulation of translational fidelity / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / translation regulator activity / stress granule assembly / rough endoplasmic reticulum / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / gastrulation / MDM2/MDM4 family protein binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / translation initiation factor binding / Glycogen synthesis / cytosolic ribosome / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 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_32800.map.gz | 106.2 MB | EMDB map data format | |
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Header (meta data) | emd-32800-v30.xml emd-32800.xml | 52.8 KB 52.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32800_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_32800.png | 163.9 KB | ||
Filedesc metadata | emd-32800.cif.gz | 12.5 KB | ||
Others | emd_32800_additional_1.map.gz emd_32800_additional_2.map.gz emd_32800_additional_3.map.gz | 107.8 MB 107.8 MB 116.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32800 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32800 | HTTPS FTP |
-Validation report
Summary document | emd_32800_validation.pdf.gz | 458.7 KB | Display | EMDB validaton report |
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Full document | emd_32800_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | emd_32800_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_32800_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32800 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32800 | HTTPS FTP |
-Related structure data
Related structure data | 7wttMC 7wtnC 7wtoC 7wtpC 7wtqC 7wtrC 7wtsC 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_32800.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: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #3
File | emd_32800_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_32800_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_32800_additional_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yeast pre-40S ribosomal subunit
+Supramolecule #1: Yeast pre-40S ribosomal subunit
+Macromolecule #1: 18S rRNA
+Macromolecule #2: 40S ribosomal protein S17
+Macromolecule #3: 40S ribosomal protein S27
+Macromolecule #4: 40S ribosomal protein S3a
+Macromolecule #5: 40S ribosomal protein S28
+Macromolecule #6: 40S ribosomal protein S4, X isoform
+Macromolecule #7: 40S ribosomal protein S30
+Macromolecule #8: 40S ribosomal protein S5
+Macromolecule #9: 40S ribosomal protein S7
+Macromolecule #10: 40S ribosomal protein S6
+Macromolecule #11: 40S ribosomal protein S25
+Macromolecule #12: 40S ribosomal protein S24
+Macromolecule #13: RNA-binding protein PNO1
+Macromolecule #14: 40S ribosomal protein S23
+Macromolecule #15: Bystin
+Macromolecule #16: 40S ribosomal protein S15a
+Macromolecule #17: Pre-rRNA-processing protein TSR1 homolog
+Macromolecule #18: Protein LTV1 homolog
+Macromolecule #19: 40S ribosomal protein S19
+Macromolecule #20: 40S ribosomal protein S18
+Macromolecule #21: 40S ribosomal protein S16
+Macromolecule #22: 40S ribosomal protein S15
+Macromolecule #23: 40S ribosomal protein S14
+Macromolecule #24: 40S ribosomal protein S13
+Macromolecule #25: 40S ribosomal protein S11
+Macromolecule #26: 40S ribosomal protein S9
+Macromolecule #27: 40S ribosomal protein S8
+Macromolecule #28: Multifunctional methyltransferase subunit TRM112-like protein
+Macromolecule #29: Probable 18S rRNA (guanine-N(7))-methyltransferase
+Macromolecule #30: RRP12-like protein
+Macromolecule #31: 40S ribosomal protein S12
+Macromolecule #32: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #33: Casein kinase I isoform alpha
+Macromolecule #34: Ribosome biogenesis protein SLX9 homolog
+Macromolecule #35: S-ADENOSYL-L-HOMOCYSTEINE
+Macromolecule #36: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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 |