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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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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 / tRNA modification in the nucleus and cytosol / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of NLRP3 inflammasome complex assembly / intermediate filament cytoskeleton organization ...peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / Activation of SMO / tRNA modification in the nucleus and cytosol / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of NLRP3 inflammasome complex assembly / intermediate filament cytoskeleton organization / Methylation / trophectodermal cell differentiation / protein methyltransferase activity / cellular response to nutrient / positive regulation of rRNA processing / tRNA methylation / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / : / beta-catenin destruction complex / negative regulation of RNA splicing / 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 / neural crest cell differentiation / rRNA methylation / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / Disassembly of the destruction complex and recruitment of AXIN to the membrane / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Maturation of nucleoprotein / U3 snoRNA binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / Translation initiation complex formation / positive regulation of Rho protein signal transduction / snoRNA binding / fibroblast growth factor binding / Protein hydroxylation / Golgi organization / 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 / monocyte chemotaxis / 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 / TOR signaling / negative regulation of respiratory burst involved in inflammatory response / L13a-mediated translational silencing of Ceruloplasmin expression / Nuclear events stimulated by ALK signaling in cancer / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / ribosomal small subunit export from nucleus / 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 / 90S preribosome / positive regulation of cell cycle / stress granule assembly / rough endoplasmic reticulum / Mitotic Prometaphase / translation initiation factor binding / EML4 and NUDC in mitotic spindle formation / Maturation of protein E / Maturation of protein E / MDM2/MDM4 family protein binding / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / transcription initiation-coupled chromatin remodeling / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / cytosolic ribosome / translational initiation / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Resolution of Sister Chromatid Cohesion / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of TORC1 signaling Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (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 | 50 KB 50 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 | ||
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 |
-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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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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Density Histograms |
-Additional map: #2
File | emd_32800_additional_2.map | ||||||||||||
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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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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 |