6RXX

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 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
Utp3B [auth UC]648Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S4H3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Utp6C [auth UF]414Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Utp7D [auth UG]558Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11E [auth UK]270Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Utp12F [auth UL]962Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Utp13G [auth UM]912Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Utp14H [auth UN]938Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Utp18I [auth UR]618Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Putative U3 snoRNP proteinJ [auth UU]1,049Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Utp24K [auth UX]193Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Imp3L [auth CJ]183Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoproteinM [auth CK]297Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoprotein proteinN [auth CL]785Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Sof1O [auth CM]446Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Emg1P [auth CN],
Q [auth CO]
252Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
KRR1 small subunit processome componentR [auth CP]322Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1S [auth CQ]259Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1T [auth Ca]255Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s5-like proteinU [auth Cc]212Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7V [auth Ce]203Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s9-like proteinW [auth Cg]190Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13-like proteinX [auth Ch]151Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-like proteinY [auth Ci]150Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-like proteinZ [auth Cj]143Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-like proteinAA [auth Cm]130Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s23-like proteinBA [auth Cn]145Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-like proteinCA [auth Cp]68Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein s27-like proteinDA [auth Cq]82Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Faf1EA [auth CU]311Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 22GA [auth UV]1,171Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Rrp7HA [auth CV]322Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal proteinIA [auth Cl]156Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinJA [auth CH]411Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Bms1KA [auth CI]1,163Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Kre33LA [auth CR],
MA [auth CS]
1,073Thermochaetoides thermophilaMutation(s): 0 
EC: 2.3.1
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4NA [auth Cb]264Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6OA [auth Cd]239Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8PA [auth Cf]202Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-like proteinQA [auth Ck]161Thermochaetoides thermophilaMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24RA [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: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein ENP2SA [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: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Utp20TA [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: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Bfr2UA [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: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Utp2VA [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: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Utp4WA [auth UD]884Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SCT7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
UTP10XA [auth UJ]1,802Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S5L1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Utp15YA [auth UO]557Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SEI5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Utp17ZA [auth UQ]960Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SCS8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Enp1AB [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: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Utp5BB [auth UI],
EB [auth UE]
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: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Utp16CB [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: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Utp8DB [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
Noc4FB [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: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Nop1GB [auth CA],
HB [auth CB]
313Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SGY2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Putative nucleolar proteinIB [auth CC]523Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S2U4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Nop58JB [auth CD]582Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RYF6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Snu13KB [auth CE],
LB [auth CF]
127Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SGM0 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Rrp9MB [auth CG]630Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SG51 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Fcf2NB [auth CT]203Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0S4E3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-like proteinPB [auth Cr]153Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0SFK8 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 31
MoleculeChains LengthOrganismImage
35S ribosomal RNAFA [auth C1]1,859Thermochaetoides thermophila
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Entity ID: 62
MoleculeChains LengthOrganismImage
U3 snoRNAOB [auth C2]232Thermochaetoides thermophila
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 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