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- PDB-8i9x: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal ... -
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Basic information
Entry | Database: PDB / ID: 8i9x | ||||||
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Title | Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-1 | ||||||
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![]() | RIBOSOME / Ribosome biogenesis / pre-60S ribosome | ||||||
Function / homology | ![]() Noc1p-Noc2p complex / Noc2p-Noc3p complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine ...Noc1p-Noc2p complex / Noc2p-Noc3p complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine / PeBoW complex / tRNA methylation / rRNA base methylation / protein kinase regulator activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / DNA replication initiation / protein-RNA complex assembly / mRNA transport / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / translation initiation factor activity / cellular response to amino acid starvation / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / nuclear periphery / post-translational protein modification / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cytosolic ribosome assembly / rRNA processing / transcription corepressor activity / ribosome biogenesis / regulation of translation / histone binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / chromatin binding / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
![]() | Lau, B. / Huang, Z. / Beckmann, R. / Hurt, E. / Cheng, J. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.7 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 311.8 KB | Display | |
Data in CIF | ![]() | 544.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35287MC ![]() 8i9pC ![]() 8i9rC ![]() 8i9tC ![]() 8i9vC ![]() 8i9wC ![]() 8i9yC ![]() 8i9zC ![]() 8ia0C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 2 types, 2 molecules C1C2
#1: RNA chain | Mass: 1079977.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 25S rRNA / Source: (natural) ![]() |
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#2: RNA chain | Mass: 102607.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 5.8S rRNA / Source: (natural) ![]() |
-Protein , 19 types, 19 molecules CACECFCGCHCICJCLCNCOCPCRCSCTCXCYCbLhLq
#3: Protein | Mass: 36482.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#7: Protein | Mass: 66830.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 30551.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 20685.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 75621.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 45884.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 77167.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 61523.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#16: Protein | Mass: 26468.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein | Mass: 13262.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#18: Protein | Mass: 83658.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#20: Protein | Mass: 26960.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#21: Protein | Mass: 95510.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#22: Protein | Mass: 77953.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 22678.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 89766.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#27: Protein | Mass: 102993.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#54: Protein | Mass: 105169.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#59: Protein | Mass: 24055.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Ribosome biogenesis protein ... , 5 types, 5 molecules CBCCCDCKCQ
#4: Protein | Mass: 43700.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#5: Protein | Mass: 90997.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 52989.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 29724.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#19: Protein | Mass: 26434.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+60S ribosomal protein ... , 24 types, 25 molecules CMLFLBLCLELGLHLKLLLMLOLPLSLTLULVLXLYLZLcLeLfLiLkLl
-RRNA-processing ... , 2 types, 2 molecules CUCz
#23: Protein | Mass: 50255.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#28: Protein | Mass: 14710.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Putative 60S ribosomal ... , 2 types, 2 molecules CVLd
#24: Protein | Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#50: Protein | Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Ribosomal protein ... , 5 types, 5 molecules LNLQLRLgLj
#37: Protein | Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#40: Protein | Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#41: Protein | Mass: 317092.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#53: Protein | Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#56: Protein | Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 2 types, 3 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#60: Chemical | ChemComp-GTP / |
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#61: Chemical |
-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 |
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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 |
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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: ![]() |
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) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77844 / Symmetry type: POINT |