6RXU

Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration.

Cheng, J.Bassler, J.Fischer, P.Lau, B.Kellner, N.Kunze, R.Griesel, S.Kallas, M.Berninghausen, O.Strauss, D.Beckmann, R.Hurt, E.

(2019) Mol Cell 75: 1256-1269.e7

  • DOI: https://doi.org/10.1016/j.molcel.2019.06.032
  • Primary Citation of Related Structures:  
    6RXT, 6RXU, 6RXV, 6RXX, 6RXY, 6RXZ

  • PubMed Abstract: 

    Eukaryotic ribosome biogenesis involves RNA folding and processing that depend on assembly factors and small nucleolar RNAs (snoRNAs). The 90S (SSU-processome) is the earliest pre-ribosome structurally analyzed, which was suggested to assemble stepwise along the growing pre-rRNA from 5' > 3', but this directionality may not be accurate. Here, by analyzing the structure of a series of 90S assembly intermediates from Chaetomium thermophilum, we discover a reverse order of 18S rRNA subdomain incorporation. Large parts of the 18S rRNA 3' and central domains assemble first into the 90S before the 5' domain is integrated. This final incorporation depends on a contact between a heterotrimer Enp2-Bfr2-Lcp5 recruited to the flexible 5' domain and Kre33, which reconstitutes the Kre33-Enp-Brf2-Lcp5 module on the compacted 90S. Keeping the 5' domain temporarily segregated from the 90S scaffold could provide extra time to complete the multifaceted 5' domain folding, which depends on a distinct set of snoRNAs and processing factors.


  • Organizational Affiliation

    Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2-like proteinA [auth UA]904Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SF93 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Utp2B [auth UB]907Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SDW0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Utp3C [auth UC]648Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Utp4D [auth UD]884Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Utp6E [auth UF]414Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Utp7F [auth UG]558Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
UTP10G [auth UJ]1,802Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11H [auth UK]270Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Utp12I [auth UL]962Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Utp13J [auth UM]912Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Utp14K [auth UN]938Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Utp15L [auth UO]557Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Utp17M [auth UQ]960Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Utp18N [auth UR]618Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Putative U3 snoRNP proteinO [auth UU]1,049Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Utp24P [auth UX]193Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Utp30Q [auth UZ]391Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Nop1R [auth CA],
S [auth CB]
313Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Nop56T [auth CC]523Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Nop58U [auth CD]582Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Snu13V [auth CE],
W [auth CF]
127Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Rrp9X [auth CG]630Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinY [auth CH]411Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Bms1Z [auth CI]1,163Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Imp3AA [auth CJ]183Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoproteinBA [auth CK]297Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoprotein proteinCA [auth CL]785Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Sof1DA [auth CM]446Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Emg1EA [auth CN],
FA [auth CO]
252Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
KRR1 small subunit processome componentGA [auth CP]322Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1HA [auth CQ]259Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Kre33IA [auth CR],
JA [auth CS]
1,073Thermochaetoides thermophilaMutation(s): 0 
EC: 2.3.1
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Fcf2KA [auth CT]203Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1LA [auth Ca]255Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4MA [auth Cb]264Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s5-like proteinNA [auth Cc]212Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6OA [auth Cd]239Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7PA [auth Ce]203Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8QA [auth Cf]202Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s9-like proteinRA [auth Cg]190Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13-like proteinSA [auth Ch]151Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-like proteinTA [auth Ci]150Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SFL1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-like proteinUA [auth Cj]143Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SBR7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-like proteinVA [auth Ck]161Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SF00 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-like proteinWA [auth Cm]130Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SHI0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s23-like proteinXA [auth Cn]145Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RY17 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24YA [auth Co]136Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for P0CU28 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-like proteinZA [auth Cp]68Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S9M9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Faf1AB [auth CU]311Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S5F1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ENP2DB [auth CW]668Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S902 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Utp20EB [auth UT]2,612Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SHP3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Utp8FB [auth UH]930Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for P0CT47 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Utp5GB [auth UE],
MB [auth UI]
410Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RYX2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Noc4HB [auth US]549Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RZL4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal proteinIB [auth Cl]156Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S6J7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Enp1JB [auth CX]480Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S5J4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein lcp5-like proteinKB [auth CY]381Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S7Z2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Bfr2LB [auth CZ]609Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SAJ6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Utp16NB [auth UP]364Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S612 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 50
MoleculeChains LengthOrganismImage
35S rRNABB [auth C1]2,352Thermochaetoides thermophila
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Entity ID: 51
MoleculeChains LengthOrganismImage
U3 snoRNACB [auth C2]230Thermochaetoides thermophila
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection, Database references