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Yorodumi- PDB-8i9t: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i9t | ||||||
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Title | Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-1 | ||||||
Components |
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Keywords | RIBOSOME / Ribosome biogenesis / pre-60S ribosome | ||||||
Function / homology | Function and homology information tRNA (cytidine-5-)-methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / intracellular mRNA localization / PeBoW complex / tRNA methylation / rRNA base methylation ...tRNA (cytidine-5-)-methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / intracellular mRNA localization / PeBoW complex / tRNA methylation / rRNA base methylation / rRNA primary transcript binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / preribosome, small subunit precursor / protein glycosylation / ribosomal large subunit binding / preribosome, large subunit precursor / nuclear-transcribed mRNA catabolic process / mRNA transport / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / ribosomal large subunit biogenesis / nuclear periphery / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / rRNA processing / ribosomal small subunit biogenesis / large ribosomal subunit / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / RNA helicase activity / negative regulation of translation / rRNA binding / RNA helicase / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Lau, B. / Huang, Z. / Beckmann, R. / Hurt, E. / Cheng, J. | ||||||
Funding support | 1items
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Citation | Journal: EMBO Rep / Year: 2023 Title: Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis. Authors: Benjamin Lau / Zixuan Huang / Nikola Kellner / Shuangshuang Niu / Otto Berninghausen / Roland Beckmann / Ed Hurt / Jingdong Cheng / Abstract: Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ...Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i9t.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8i9t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8i9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i9t_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8i9t_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8i9t_validation.xml.gz | 271.2 KB | Display | |
Data in CIF | 8i9t_validation.cif.gz | 458.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/8i9t ftp://data.pdbj.org/pub/pdb/validation_reports/i9/8i9t | HTTPS FTP |
-Related structure data
Related structure data | 35283MC 8i9pC 8i9rC 8i9vC 8i9wC 8i9xC 8i9yC 8i9zC 8ia0C 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
+RNA chain , 3 types, 3 molecules C1C2C3
+Brix domain-containing ... , 3 types, 3 molecules CACdCg
+Ribosome biogenesis protein ... , 4 types, 4 molecules CBCCCKCQ
+Protein , 16 types, 16 molecules CECFCHCICJCLCNCOCPCRCSCXCbLhLqCe
+60S ribosome ... , 2 types, 2 molecules CGCf
+60S ribosomal protein ... , 19 types, 20 molecules CMLFLBLCLELGLHLKLLLMLOLPLSLTLVLXLYLeLfLi
+RRNA-processing ... , 2 types, 2 molecules CUCz
+Ribosomal RNA-processing protein ... , 2 types, 2 molecules ChCc
+Ribosomal protein ... , 3 types, 3 molecules LNLQLj
+Non-polymers , 2 types, 4 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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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 | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52677 / Symmetry type: POINT |