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- EMDB-32802: Cryo-EM structure of a human pre-40S ribosomal subunit - State RR... -
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Basic information
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Title | Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A2 | |||||||||
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![]() | ribosome biogenesis / 40S ribosome / RIBOSOME | |||||||||
Function / homology | ![]() peptidyl-glutamine methylation / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / regulation of protein localization to nucleolus / 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 ...peptidyl-glutamine methylation / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / regulation of protein localization to nucleolus / 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 / rRNA methylation / negative regulation of RNA splicing / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neural crest cell differentiation / positive regulation of ubiquitin-protein transferase activity / U3 snoRNA binding / negative regulation of bicellular tight junction assembly / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / snoRNA binding / laminin receptor activity / preribosome, small subunit precursor / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / fibroblast growth factor binding / monocyte chemotaxis / Protein hydroxylation / TOR signaling / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / cellular response to ethanol / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / Maturation of protein E / Maturation of protein E / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / L13a-mediated translational silencing of Ceruloplasmin expression / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / 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) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of translational fidelity / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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) / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Protein methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / maturation of LSU-rRNA / Regulation of PTEN localization / Nuclear events stimulated by ALK signaling in cancer Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Cheng J / Lau B / Thoms M / Ameismeier M / Berninghausen O / Hurt E / Beckmann R | |||||||||
Funding support | 1 items
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![]() | ![]() 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. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 104.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 53.2 KB 53.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 151.4 KB | ||
Filedesc metadata | ![]() | 12.4 KB | ||
Others | ![]() ![]() ![]() ![]() | 105 MB 70.2 MB 119.3 MB 118.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 460.4 KB | Display | ![]() |
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Full document | ![]() | 460 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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: #4
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-Additional map: #3
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-Additional map: #2
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-Additional map: #1
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Density Histograms |
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |