5OQL

Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history


Literature

3.2- angstrom -resolution structure of the 90S preribosome before A1 pre-rRNA cleavage.

Cheng, J.Kellner, N.Berninghausen, O.Hurt, E.Beckmann, R.

(2017) Nat Struct Mol Biol 24: 954-964

  • DOI: https://doi.org/10.1038/nsmb.3476
  • Primary Citation of Related Structures:  
    5OQL

  • PubMed Abstract: 

    The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophilum 90S preribosome, which allowed us to build atomic structures for 34 assembly factors, including the Mpp10 complex, Bms1, Utp14 and Utp18, and the complete U3 small nucleolar ribonucleoprotein. Moreover, we visualized the U3 RNA heteroduplexes with a 5' external transcribed spacer (5' ETS) and pre-18S RNA, and their stabilization by 90S factors. Overall, the structure explains how a highly intertwined network of assembly factors and pre-rRNA guide the sequential, independent folding of the individual pre-40S domains while the RNA regions forming the 40S active sites are kept immature. Finally, by identifying the unprocessed A1 cleavage site and the nearby Utp24 endonuclease, we suggest a proofreading model for regulated 5'-ETS separation and 90S-pre-40S transition.


  • Organizational Affiliation

    Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2-like protein904Thermochaetoides thermophila DSM 1495Mutation(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
Utp2907Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Utp3648Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Utp4884Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Utp6414Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S387 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Utp7558Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Utp101,802Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S5L1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11270Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Utp12962Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Utp13912Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Utp14938Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Utp15557Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Utp17960Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Utp18618Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Putative U3 snoRNP protein1,049Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Utp24194Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Utp30391Thermochaetoides 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: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Nop1
R, S
313Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Putative nucleolar protein523Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S2U4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Nop58582Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Snu13
V, W
127Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Rrp9630Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like protein411Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Bms11,163Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Imp3AA [auth a]183Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoproteinBA [auth b]297Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Putative U3 small nucleolar ribonucleoprotein proteinCA [auth c]785Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Sof1DA [auth d]446Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Emg1EA [auth e],
FA [auth f]
252Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
KRR1 small subunit processome componentGA [auth g]322Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1HA [auth h]259Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RNA cytidine acetyltransferaseIA [auth i],
JA [auth j]
1,073Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 2.3.1
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Fcf2KA [auth k]203Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1LA [auth l]255Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4MA [auth m]264Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s5-like proteinNA [auth n]212Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6OA [auth o]239Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-like proteinPA [auth p]203Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8QA [auth q]202Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein s9-like proteinRA [auth r]190Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13-like proteinSA [auth s]151Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RZM9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0RZM9
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-like proteinTA [auth t]150Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SFL1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0SFL1
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-like proteinUA [auth u]143Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SBR7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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UniProt GroupG0SBR7
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-like proteinVA [auth v]161Thermochaetoides thermophila DSM 1495Mutation(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 w]130Thermochaetoides thermophila DSM 1495Mutation(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 x]145Thermochaetoides thermophila DSM 1495Mutation(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 y]136Thermochaetoides thermophila DSM 1495Mutation(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 z]68Thermochaetoides thermophila DSM 1495Mutation(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 0]311Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S5F1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 50
MoleculeChains LengthOrganismImage
35S rRNABB [auth 1]2,568Thermochaetoides thermophila DSM 1495
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Entity ID: 51
MoleculeChains LengthOrganismImage
U3 snoRNACB [auth 2]274Thermochaetoides thermophila DSM 1495
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
DB [auth P]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTPHENIX
MODEL REFINEMENTREFMAC

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2019-10-02
    Changes: Data collection, Other
  • Version 1.3: 2019-10-23
    Changes: Data collection, Other