6ZQF

Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-B (Poly-Ala)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 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

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

  • 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 ...

    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. beckmann@genzentrum.lmu.de ed.hurt@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periodic tryptophan protein 2A [auth UA]923Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2UTP1YCR057CYCR55C/YCR57C/YCR58C
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Entity ID: 2
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Nucleolar complex protein 14B [auth UB]810Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP14UTP2YDL148CD1566
UniProt
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Entity ID: 3
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Something about silencing protein 10C [auth UC]610Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAS10UTP3YDL153CD1545
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Entity ID: 4
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U3 small nucleolar RNA-associated protein 12D [auth UL]943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2UTP12YLR129WL3116L9233.1
UniProt
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Entity ID: 5
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U3 small nucleolar RNA-associated protein 13E [auth UM]817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13YLR222C
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Entity ID: 6
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Nucleolar complex protein 4F [auth US]552Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOC4UTP19YPR144C
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Entity ID: 7
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U3 small nucleolar RNA-associated protein 21G [auth UU]939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21YLR409CL8084.22
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Entity ID: 8
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U3 small nucleolar RNA-associated protein 22H [auth UV]1237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22YGR090W
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Entity ID: 9
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U3 small nucleolar ribonucleoprotein protein IMP3I [auth CI]183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3YHR148W
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Entity ID: 10
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U3 small nucleolar ribonucleoprotein protein IMP4J [auth CJ]290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4YNL075WN2353
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Entity ID: 11
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U3 small nucleolar RNA-associated protein MPP10K [auth CK]593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10YJR002WJ1411YJR83.5
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Entity ID: 12
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Ribosome biogenesis protein BMS1L [auth CL]1183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1YPL217C
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Entity ID: 13
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RNA 3'-terminal phosphate cyclase-like proteinM [auth CM]367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1RTC1YOL010W
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Entity ID: 14
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Ribosomal RNA-processing protein 7N [auth CN]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7YCL031CYCL184YCL31C
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Entity ID: 15
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Probable ATP-dependent RNA helicase DHR1O [auth JD]1267Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM16DHR1YMR128WYM9553.04
EC: 3.6.4.13
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Entity ID: 16
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Ribosomal RNA small subunit methyltransferase NEP1P [auth JF], Q [auth JG]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EMG1NEP1YLR186WL9470.5
EC: 2.1.1.260
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Entity ID: 17
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Essential nuclear protein 1R [auth JH]483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1MEG1YBR247CYBR1635
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Dimethyladenosine transferaseS [auth JL]318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIM1YPL266W
EC: 2.1.1.183
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Entity ID: 19
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Pre-rRNA-processing protein PNO1T [auth JJ]274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNO1DIM2RRP20YOR145CO3513YOR3513C
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Entity ID: 20
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Rps5pU [auth DF]225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 21
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40S ribosomal protein S16-AV [auth DQ]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 22
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40S ribosomal protein S18-AW [auth DS]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 23
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40S ribosomal protein S19-AX [auth DT]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 24
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40S ribosomal protein S28-AY [auth Dc]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 27
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40S ribosomal protein S1-ABA [auth DA]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 28
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40S ribosomal protein S4-ACA [auth DE]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 29
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40S ribosomal protein S6-ADA [auth DG]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 30
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40S ribosomal protein S7-AEA [auth DH]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 31
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40S ribosomal protein S8-AFA [auth DI]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 32
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40S ribosomal protein S9-AGA [auth DJ]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 33
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40S ribosomal protein S11-AHA [auth DL]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 34
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40S ribosomal protein S13IA [auth DN]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 35
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40S ribosomal protein S14-AJA [auth DO]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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Entity ID: 36
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40S ribosomal protein S25-AKA [auth DZ]108Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
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Entity ID: 37
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40S ribosomal protein S22-ALA [auth DW]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 38
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40S ribosomal protein S23-AMA [auth DX]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 39
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40S ribosomal protein S24-ANA [auth DY]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 40
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40S ribosomal protein S27-AOA [auth Db]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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  • Entity ID: 25
    MoleculeChainsLengthOrganismImage
    5ETS RNAZ [auth D2]20Saccharomyces cerevisiae S288C
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    Entity ID: 26
    MoleculeChainsLengthOrganismImage
    18S rRNAAA [auth D3]1758Saccharomyces cerevisiae S288C
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    Entity ID: 41
    MoleculeChainsLengthOrganismImage
    U3 snoRNAPA [auth D4]35Saccharomyces cerevisiae S288C
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    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    QA [auth Db]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 4.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    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