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Yorodumi- PDB-8i9v: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal ... -
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-Basic information
Entry | Database: PDB / ID: 8i9v | ||||||
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Title | Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-2 | ||||||
Components |
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Keywords | RIBOSOME / Ribosome biogenesis / pre-60S ribosome | ||||||
Function / homology | Function and homology information Noc1p-Noc2p complex / Noc2p-Noc3p complex / tRNA (cytidine-5-)-methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine ...Noc1p-Noc2p complex / Noc2p-Noc3p complex / tRNA (cytidine-5-)-methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine / 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) / preribosome, small subunit precursor / maturation of 5.8S rRNA / ribosomal large subunit binding / nuclear-transcribed mRNA catabolic process / preribosome, large subunit precursor / DNA replication initiation / 90S preribosome / mRNA transport / post-translational protein modification / ribosomal subunit export from nucleus / ribonucleoprotein complex binding / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / rRNA processing / transcription corepressor activity / ribosome biogenesis / ribosomal small subunit biogenesis / 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 / translation / ribonucleoprotein complex / chromatin binding / GTPase activity / mRNA binding / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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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PDBx/mmCIF format | 8i9v.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8i9v.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8i9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i9v_validation.pdf.gz | 885.7 KB | Display | wwPDB validaton report |
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Full document | 8i9v_full_validation.pdf.gz | 962.1 KB | Display | |
Data in XML | 8i9v_validation.xml.gz | 208.4 KB | Display | |
Data in CIF | 8i9v_validation.cif.gz | 356.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/8i9v ftp://data.pdbj.org/pub/pdb/validation_reports/i9/8i9v | HTTPS FTP |
-Related structure data
Related structure data | 35285MC 8i9pC 8i9rC 8i9tC 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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-Components
-RNA chain , 3 types, 3 molecules C1C2C3
#1: RNA chain | Mass: 1079977.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 25S rRNA / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
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#2: RNA chain | Mass: 82467.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 5.8S rRNA / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
#3: RNA chain | Mass: 51802.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ITS2 rRNA / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
-Brix domain-containing ... , 2 types, 2 molecules CACd
#4: Protein | Mass: 36482.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RXZ3 |
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#53: Protein | Mass: 49471.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4S2 |
-Ribosome biogenesis protein ... , 4 types, 4 molecules CBCCCKCQ
#5: Protein | Mass: 43700.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S7X0 |
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#6: Protein | Mass: 90838.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCK6 |
#13: Protein | Mass: 29724.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S081 |
#19: Protein | Mass: 26434.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S497 |
-Protein , 20 types, 20 molecules CECFCHCICJCLCNCOCPCRCSCTCXCYCbLdLhLqCcCe
#7: Protein | Mass: 66830.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYU9 |
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#8: Protein | Mass: 30551.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S616 |
#10: Protein | Mass: 75621.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8F1 |
#11: Protein | Mass: 45884.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1H0 |
#12: Protein | Mass: 77167.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHX6 |
#14: Protein | Mass: 61523.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEW3 |
#16: Protein | Mass: 26468.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S683 |
#17: Protein | Mass: 13262.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHK0 |
#18: Protein | Mass: 83658.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHQ0 |
#20: Protein | Mass: 26960.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S832 |
#21: Protein | Mass: 95510.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G0SGD8, Transferases; Transferring one-carbon groups; Methyltransferases |
#22: Protein | Mass: 77953.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5L0 |
#24: Protein | Mass: 22678.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGJ0 |
#25: Protein | Mass: 89766.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SD05 |
#27: Protein | Mass: 102993.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5S8, RNA helicase |
#45: Protein | Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SD68 |
#48: Protein | Mass: 105169.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#51: Protein | Mass: 24055.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4Z9 |
#52: Protein | Mass: 32128.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S4M2 |
#54: Protein | Mass: 39464.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFD6 |
-60S ribosome ... , 2 types, 2 molecules CGCf
#9: Protein | Mass: 20685.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S435 |
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#55: Protein | Mass: 64465.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S2I7 |
-60S ribosomal protein ... , 19 types, 20 molecules CMLFLBLCLELGLHLKLLLMLOLPLSLTLVLXLYLeLfLi
#15: Protein | Mass: 28821.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFL0 #28: Protein | | Mass: 44456.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RXW1 #29: Protein | | Mass: 39439.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFC3 #30: Protein | | Mass: 22132.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0D6 #31: Protein | | Mass: 29744.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SAJ9 #32: Protein | | Mass: 21582.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0E5 #33: Protein | | Mass: 17802.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGH8 #34: Protein | | Mass: 24191.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S992 #35: Protein | | Mass: 16111.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1R0 #37: Protein | | Mass: 22993.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SH61 #38: Protein | | Mass: 21072.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGY1 #40: Protein | | Mass: 20341.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCE2 #41: Protein | | Mass: 18159.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S0Z3 #42: Protein | | Mass: 14674.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SI44 #43: Protein | | Mass: 17175.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S507 #44: Protein | | Mass: 15565.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYN9 #46: Protein | | Mass: 15095.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6V4 #47: Protein | | Mass: 12330.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCL3 #49: Protein | | Mass: 12784.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SBN1 |
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-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) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGC2 |
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#26: Protein | Mass: 14710.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCP3 |
-Ribosomal protein ... , 3 types, 3 molecules LNLQLj
#36: Protein | Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZ88 |
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#39: Protein | Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9B5 |
#50: Protein | Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S101 |
-Non-polymers , 2 types, 4 molecules
#56: Chemical | ChemComp-GTP / |
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#57: 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 |
-Sample preparation
Component |
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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16465 / Symmetry type: POINT |