8I9P

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Mak16


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.

Lau, B.Huang, Z.Kellner, N.Niu, S.Berninghausen, O.Beckmann, R.Hurt, E.Cheng, J.

(2023) EMBO Rep 24: e56910-e56910

  • DOI: https://doi.org/10.15252/embr.202356910
  • Primary Citation of Related Structures:  
    8I9P, 8I9R, 8I9T, 8I9V, 8I9W, 8I9X, 8I9Y, 8I9Z, 8IA0

  • PubMed 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 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.


  • Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Brix domain-containing proteinC [auth CA]316Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RXZ3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein C8F11.04D [auth CB]391Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S7X0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ERB1E [auth CC]801Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SCK6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA helicaseF [auth CE]598Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RYU9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Putative RNA-binding proteinG [auth CI]414Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologH [auth CJ]679Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l7-like proteinI [auth CM],
N [auth LF]
249Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 16J [auth CR]237Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S832 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein EBP2K [auth CU]451Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-like proteinL [auth LC]365Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6M [auth LE]200Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8O [auth LG]262Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13P [auth LL]213Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S992 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-like proteinQ [auth LM]142Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15R [auth LN]203Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RZ88 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-like proteinS [auth LO]204Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SH61 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l17-like proteinT [auth LP]187Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SGY1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18-like proteinU [auth LQ]213Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S9B5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20V [auth LS]174Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SCE2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l21-like proteinW [auth LT]160Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S0Z3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25-like proteinX [auth LX]156Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S507 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-like proteinY [auth LY]138Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RYN9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32-like proteinZ [auth Le]131Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S6V4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l33-like proteinAA [auth Lf]109Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
dolichyl-diphosphooligosaccharide--protein glycotransferaseBA [auth Lh]935Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 2.4.99.18
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36CA [auth Li]110Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37DA [auth Lj]95Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 1EA [auth Cc]282Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Brix domain-containing proteinFA [auth Cd]436Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MAK16GA [auth Ce]336Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (3341-MER)A [auth C1]3,341Thermochaetoides thermophila DSM 1495
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (306-MER)B [auth C2]306Thermochaetoides thermophila DSM 1495
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references