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Yorodumi- PDB-7wtq: Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Ts... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wtq | ||||||
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Title | Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-2 (without Rps2) | ||||||
Components |
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Keywords | RIBOSOME / ribosome biogenesis / 40S ribosome | ||||||
Function / homology | Function and homology information 18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / mTORC1-mediated signalling / Protein hydroxylation ...18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / mTORC1-mediated signalling / Protein hydroxylation / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / Ub-specific processing proteases / regulation of translational fidelity / ribonucleoprotein complex binding / ribosomal small subunit export from nucleus / 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) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / unfolded protein binding / ribosomal small subunit biogenesis / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Cheng, J. / Lau, B. / Thoms, M. / Ameismeier, M. / Berninghausen, O. / Hurt, E. / Beckmann, R. | ||||||
Funding support | 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wtq.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7wtq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7wtq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wtq_validation.pdf.gz | 930 KB | Display | wwPDB validaton report |
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Full document | 7wtq_full_validation.pdf.gz | 1009.3 KB | Display | |
Data in XML | 7wtq_validation.xml.gz | 106.2 KB | Display | |
Data in CIF | 7wtq_validation.cif.gz | 179.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/7wtq ftp://data.pdbj.org/pub/pdb/validation_reports/wt/7wtq | HTTPS FTP |
-Related structure data
Related structure data | 32795MC 7wtnC 7wtoC 7wtpC 7wtrC 7wtsC 7wttC 7wtuC 7wtvC 7wtwC 7wtxC 7wtzC 7wu0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-40S ribosomal protein ... , 14 types, 14 molecules SBSESGSHSISJSLSNSOSWSXSYSbSe
#2: Protein | Mass: 28798.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33442 |
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#3: Protein | Mass: 29469.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX35 |
#4: Protein | Mass: 27054.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX37 |
#5: Protein | Mass: 21658.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P26786 |
#6: Protein | Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX39 |
#7: Protein | Mass: 22487.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: O13516 |
#8: Protein | Mass: 17785.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX47 |
#9: Protein | Mass: 17059.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P05756 |
#10: Protein | Mass: 14562.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P06367 |
#11: Protein | Mass: 14650.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1 |
#12: Protein | Mass: 16073.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX29 |
#13: Protein | Mass: 15362.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX31 |
#14: Protein | Mass: 8893.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P35997 |
#15: Protein | Mass: 7137.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P0CX33 |
-Protein , 3 types, 3 molecules CACBCC
#16: Protein | Mass: 30380.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q99216 |
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#17: Protein | Mass: 30788.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P25627, 18S rRNA (guanine1575-N7)-methyltransferase |
#18: Protein | Mass: 90876.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q07381 |
-RNA chain / Non-polymers , 2 types, 2 molecules C2
#19: Chemical | ChemComp-ZN / |
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#1: RNA chain | Mass: 579761.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Yeast pre-40S ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#18 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Details: Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39865 / Symmetry type: POINT |