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Yorodumi- EMDB-32802: Cryo-EM structure of a human pre-40S ribosomal subunit - State RR... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32802 | |||||||||
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Title | Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A2 | |||||||||
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 / tRNA modification in the nucleus and cytosol / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Methylation / trophectodermal cell differentiation / protein methyltransferase activity ...peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / tRNA modification in the nucleus and cytosol / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Methylation / trophectodermal cell differentiation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / : / negative regulation of RNA splicing / laminin receptor activity / neural crest cell differentiation / rRNA methylation / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / 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 / snoRNA binding / fibroblast growth factor binding / 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Selenocysteine synthesis / monocyte chemotaxis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ribosomal small subunit export from nucleus / 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 / negative regulation of respiratory burst involved in inflammatory response / L13a-mediated translational silencing of Ceruloplasmin expression / 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) / regulation of translational fidelity / rough endoplasmic reticulum / Major pathway of rRNA processing in the nucleolus and cytosol / MDM2/MDM4 family protein binding / laminin binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Protein methylation / 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 / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / EML4 and NUDC in mitotic spindle formation / maturation of SSU-rRNA / Maturation of protein E / Maturation of protein E / negative regulation of ubiquitin-dependent protein catabolic process / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / transcription initiation-coupled chromatin remodeling / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / 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) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Resolution of Sister Chromatid Cohesion / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 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_32802.map.gz | 104.4 MB | EMDB map data format | |
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Header (meta data) | emd-32802-v30.xml emd-32802.xml | 50.3 KB 50.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32802_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_32802.png | 151.4 KB | ||
Others | emd_32802_additional_1.map.gz emd_32802_additional_2.map.gz emd_32802_additional_3.map.gz emd_32802_additional_4.map.gz | 105 MB 70.2 MB 119.3 MB 118.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32802 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32802 | HTTPS FTP |
-Related structure data
Related structure data | 7wtvMC 7wtnC 7wtoC 7wtpC 7wtqC 7wtrC 7wtsC 7wttC 7wtuC 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_32802.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: #4
File | emd_32802_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: #3
File | emd_32802_additional_2.map | ||||||||||||
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-Additional map: #2
File | emd_32802_additional_3.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_32802_additional_4.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: 40S ribosomal protein S19
+Macromolecule #19: 40S ribosomal protein S18
+Macromolecule #20: 40S ribosomal protein S16
+Macromolecule #21: 40S ribosomal protein S15
+Macromolecule #22: 40S ribosomal protein S14
+Macromolecule #23: 40S ribosomal protein S13
+Macromolecule #24: 40S ribosomal protein S11
+Macromolecule #25: 40S ribosomal protein S9
+Macromolecule #26: 40S ribosomal protein S8
+Macromolecule #27: Multifunctional methyltransferase subunit TRM112-like protein
+Macromolecule #28: Probable 18S rRNA (guanine-N(7))-methyltransferase
+Macromolecule #29: RRP12-like protein
+Macromolecule #30: 40S ribosomal protein S12
+Macromolecule #31: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #32: Ribosome biogenesis protein SLX9 homolog
+Macromolecule #33: 40S ribosomal protein SA
+Macromolecule #34: 40S ribosomal protein S2
+Macromolecule #35: 40S ribosomal protein S21
+Macromolecule #36: ZINC ION
+Macromolecule #37: S-ADENOSYL-L-HOMOCYSTEINE
-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 |