6ZQD

Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Post-A1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

90 S pre-ribosome transformation into the primordial 40 S subunit.

Cheng, J., Lau, B., La Venuta, G., Ameismeier, M., Berninghausen, O., Hurt, E., Beckmann, R.

(2020) Science 369: 1470-1476

  • DOI: https://doi.org/10.1126/science.abb4119
  • Primary Citation of Related Structures:  
    6ZQA, 6ZQB, 6ZQC, 6ZQD, 6ZQE, 6ZQF, 6ZQG

  • PubMed Abstract: 

    Production of small ribosomal subunits initially requires the formation of a 90 S precursor followed by an enigmatic process of restructuring into the primordial pre-40 S subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 S pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A 1 , thereby separating the 5'-external transcribed spacer (ETS) from 18 S ribosomal RNA. Next, the 5'-ETS and 90 S assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 S emerges, still retaining some 90 S factors including Dhr1, now ready to unwind the final small nucleolar U3-18 S RNA hybrid. Our data shed light on the elusive 90 S to pre-40 S transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.

    • Organizational Affiliation: 

    Gene Center, Department of Biochemistry, University of Munich, 81377 Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2A [auth UA]923Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 14B [auth UB]810Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q99207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Something about silencing protein 10C [auth UC]610Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 4D [auth UD]776Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 5E [auth UE]643Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 6F [auth UF]440Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 7G [auth UG]554Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 8H [auth UH]713Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 9I [auth UI]575Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 10J [auth UJ]1,769Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 11K [auth UK]250Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 12L [auth UL]943Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 13M [auth UM]817Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14N [auth UN]899Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 15O [auth UO]513Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Bud site selection protein 21P [auth UP]214Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for Q08492 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NET1-associated nuclear protein 1Q [auth UQ]896Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18R [auth UR]594Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for P40362 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar complex protein 4S [auth US]552Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for Q06512 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20T [auth UT]2,493Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for P35194 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21U [auth UU]939Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 22V [auth UV]1,237Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1W [auth UX]189Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinX [auth CA],
Y [auth CB]		327Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56Z [auth CD]504Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58AA [auth CE]511Saccharomyces cerevisiae S288CMutation(s): 0 
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Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinBA [auth CF],
CA [auth CG]		126Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9DA [auth CH]573Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3EA [auth CI]183Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4FA [auth CJ]290Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein MPP10GA [auth CK]593Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P47083 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1HA [auth CL]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinIA [auth CM]367Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 7JA [auth CN]297Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DHR1KA [auth JD]1,267Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.6.4.13
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1LA [auth JF],
MA [auth JG]		252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.260
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Essential nuclear protein 1NA [auth JH]483Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA biogenesis protein RRP5OA [auth JI]1,729Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Dimethyladenosine transferasePA [auth JL]318Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.183
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF2QA [auth JM]217Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SOF1RA [auth JP]489Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-ASA [auth Db]82Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1TA [auth JJ]274Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q99216 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AUA [auth DA]255Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AVA [auth DE]261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pWA [auth DF]225Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AXA [auth DG]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AYA [auth DH]190Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AZA [auth DI]200Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AAB [auth DJ]197Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-ABB [auth DL]156Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13CB [auth DN]151Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-ADB [auth DO]137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AEB [auth DQ]143Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AFB [auth DS]146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AGB [auth DT]144Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AHB [auth DW]130Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AIB [auth DX]145Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AJB [auth DY]135Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AKB [auth Dc]67Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains LengthOrganismImage
5ETS RNALB [auth D2]81Saccharomyces cerevisiae S288C
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Entity ID: 62
MoleculeChains LengthOrganismImage
18S rRNAMB [auth D3]1,802Saccharomyces cerevisiae S288C
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Entity ID: 63
MoleculeChains LengthOrganismImage
U3 snoRNANB [auth D4]333Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references