8I9R

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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
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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
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RNA helicaseF [auth CE]598Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1G [auth CH]661Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Putative RNA-binding proteinH [auth CI]414Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pescadillo homologI [auth CJ]679Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l7-like proteinJ [auth CM],
S [auth LF]
249Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6K [auth CN]246Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24L [auth CQ]225Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 16M [auth CR]237Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein EBP2N [auth CU]451Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 15O [auth Ch]354Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S5P7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3-like proteinP [auth LB]392Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-like proteinQ [auth LC]365Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6R [auth LE]200Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8T [auth LG]262Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SAJ9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13U [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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-like proteinV [auth LM]142Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S1R0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15W [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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-like proteinX [auth LO]204Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l17-like proteinY [auth LP]187Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18-like proteinZ [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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20AA [auth LS]174Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l21-like proteinBA [auth LT]160Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l23-like proteinCA [auth LV]139Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-like proteinDA [auth LY]138Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32-like proteinEA [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: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l33-like proteinFA [auth Lf]109Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
dolichyl-diphosphooligosaccharide--protein glycotransferaseGA [auth Lh]935Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 2.4.99.18
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36HA [auth Li]110Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37IA [auth Lj]95Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 1JA [auth Cc]282Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Brix domain-containing proteinKA [auth Cd]436Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MAK16LA [auth Ce]336Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosome biogenesis protein Rrp14MA [auth Cf]570Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome production factor 2 homologNA [auth Cy]350Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Brix domain-containing proteinOA [auth Cg]478Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
RNA methyltransferase nop2-like proteinPA [auth CP]751Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosome subunit biogenesis protein NIP7QA [auth CG]184Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S435 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0S435
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinRA [auth Lq]217Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S4Z9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0S4Z9
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis regulatory proteinSA [auth Cx]202Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SCH6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal proteinTA [auth LJ]173Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SHQ2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein l5-like proteinUA [auth LD]304Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SEG2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0SEG2
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal subunit-like proteinWA [auth CX]203Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SGJ0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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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 (256-MER)B [auth C2]256Thermochaetoides thermophila DSM 1495
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Entity ID: 47
MoleculeChains LengthOrganismImage
RNA (119-MER)VA [auth C4]119Thermochaetoides thermophila DSM 1495
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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: Data collection, Database references