7AJU

Cryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome)


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 1.1 of the entry. See complete history


Literature

Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome.

Lau, B.Cheng, J.Flemming, D.La Venuta, G.Berninghausen, O.Beckmann, R.Hurt, E.

(2021) Mol Cell 81: 293

  • DOI: 10.1016/j.molcel.2020.11.009
  • Primary Citation of Related Structures:  
    7AJT, 7AJU

  • PubMed Abstract: 
  • Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in this progression is removal of the 5' external transcribed spacer (5'-ETS), an RNA extension at the 18S rRNA that is integrated into the huge 90S pre-ribosome structure ...

    Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in this progression is removal of the 5' external transcribed spacer (5'-ETS), an RNA extension at the 18S rRNA that is integrated into the huge 90S pre-ribosome structure. Upon endo-nucleolytic cleavage at an internal site, A 1 , the 5'-ETS is separated from the 18S rRNA and degraded. Here we present biochemical and cryo-electron microscopy analyses that depict the RNA exosome, a major 3'-5' exoribonuclease complex, in a super-complex with the 90S pre-ribosome. The exosome is docked to the 90S through its co-factor Mtr4 helicase, a processive RNA duplex-dismantling helicase, which strategically positions the exosome at the base of 5'-ETS helices H9-H9', which are dislodged in our 90S-exosome structures. These findings suggest a direct role of the exosome in structural remodeling of the 90S pre-ribosome to drive eukaryotic ribosome synthesis.


    Organizational Affiliation

    Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany. Electronic address: ed.hurt@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinA [auth CA],
D [auth CB]
327Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP1LOT3YDL014WD2870
EC: 2.1.1
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Entity ID: 2
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40S ribosomal protein S1-AB [auth DA]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 3
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Periodic tryptophan protein 2C [auth UA]923Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2UTP1YCR057CYCR55C/YCR57C/YCR58C
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Nucleolar complex protein 14E [auth UB]810Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP14UTP2YDL148CD1566
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Entity ID: 5
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Something about silencing protein 10F [auth UC]610Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAS10UTP3YDL153CD1545
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U3 small nucleolar RNA-associated protein 4G [auth UD]776Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP4YDR324C
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Entity ID: 7
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U3 small nucleolar RNA-associated protein 5H [auth UE]643Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP5YDR398WD9509.17
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U3 small nucleolar RNA-associated protein 6I [auth UF]440Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP6YDR449CD9461.34
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U3 small nucleolar RNA-associated protein 7J [auth UG]554Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP7KRE31YER082C
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U3 small nucleolar RNA-associated protein 8K [auth UH]713Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP8YGR128C
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Entity ID: 11
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U3 small nucleolar RNA-associated protein 9L [auth UI]575Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP9YHR196W
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U3 small nucleolar RNA-associated protein 10M [auth UJ]1,769Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP10YJL109CJ0808
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U3 small nucleolar RNA-associated protein 11N [auth UK]250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP11YKL099CYKL449
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U3 small nucleolar RNA-associated protein 12O [auth UL]943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2UTP12YLR129WL3116L9233.1
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Entity ID: 15
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U3 small nucleolar RNA-associated protein 13P [auth UM]817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13YLR222C
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Entity ID: 16
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U3 small nucleolar RNA-associated protein 14Q [auth UN]899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP14YML093W
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Entity ID: 17
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U3 small nucleolar RNA-associated protein 15R [auth UO]513Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP15YMR093WYM9582.18
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Entity ID: 18
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Bud site selection protein 21S [auth UP]214Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD21UTP16YOR078WYOR29-29
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Entity ID: 19
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NET1-associated nuclear protein 1T [auth UQ]896Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAN1UTP17YPL126W
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Entity ID: 20
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U3 small nucleolar RNA-associated protein 18U [auth UR]594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP18YJL069CHRE594J1098
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Nucleolar complex protein 4V [auth US]552Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOC4UTP19YPR144C
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Entity ID: 22
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U3 small nucleolar RNA-associated protein 20W [auth UT]2,493Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP20YBL004WYBL0101
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Entity ID: 23
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U3 small nucleolar RNA-associated protein 21X [auth UU]939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21YLR409CL8084.22
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U3 small nucleolar RNA-associated protein 22Y [auth UV]1,237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22YGR090W
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rRNA-processing protein FCF1Z [auth UX]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF1YDR339CD9651.9
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Entity ID: 26
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Nucleolar protein 56AA [auth CD]504Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP56SIK1YLR197WL8167.9
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Nucleolar protein 58BA [auth CE]511Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP58NOP5YOR310CO6108
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinCA [auth CF],
DA [auth CG]
126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
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Entity ID: 29
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Ribosomal RNA-processing protein 9EA [auth CH]573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9YPR137W
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Entity ID: 30
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U3 small nucleolar ribonucleoprotein protein IMP3FA [auth CI]183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3YHR148W
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Entity ID: 31
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U3 small nucleolar ribonucleoprotein protein IMP4GA [auth CJ]290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4YNL075WN2353
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Entity ID: 32
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U3 small nucleolar RNA-associated protein MPP10HA [auth CK]593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10YJR002WJ1411YJR83.5
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Entity ID: 33
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Ribosome biogenesis protein BMS1IA [auth CL]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1YPL217C
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Entity ID: 34
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RNA 3'-terminal phosphate cyclase-like proteinJA [auth CM]367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1RTC1YOL010W
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Entity ID: 35
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Ribosomal RNA-processing protein 7KA [auth CN]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7YCL031CYCL184YCL31C
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Probable ATP-dependent RNA helicase DHR1LA [auth JD]1,267Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ECM16DHR1YMR128WYM9553.04
EC: 3.6.4.13
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Entity ID: 37
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Ribosomal RNA small subunit methyltransferase NEP1MA [auth JF],
NA [auth JG]
252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EMG1NEP1YLR186WL9470.5
EC: 2.1.1.260
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Essential nuclear protein 1OA [auth JH]483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1MEG1YBR247CYBR1635
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rRNA biogenesis protein RRP5PA [auth JI]1,729Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP5FMI1YMR229CYM9959.11C
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Entity ID: 40
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Dimethyladenosine transferaseQA [auth JL]318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIM1YPL266W
EC: 2.1.1.183
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UniProt GroupP41819
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Entity ID: 41
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rRNA-processing protein FCF2RA [auth JM]217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF2YLR051CL2128
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Entity ID: 42
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Protein SOF1SA [auth JP]489Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SOF1YLL011WL1339
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Entity ID: 43
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40S ribosomal protein S27-ATA [auth Db]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 44
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Pre-rRNA-processing protein PNO1UA [auth JJ]274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNO1DIM2RRP20YOR145CO3513YOR3513C
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Entity ID: 45
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40S ribosomal protein S4-AVA [auth DE]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 46
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40S ribosomal protein S5WA [auth DF]225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 47
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40S ribosomal protein S6-AXA [auth DG]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 48
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40S ribosomal protein S7-AYA [auth DH]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 49
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40S ribosomal protein S8-AZA [auth DI]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 50
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40S ribosomal protein S9-AAB [auth DJ]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 51
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40S ribosomal protein S11-ABB [auth DL]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 52
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40S ribosomal protein S13CB [auth DN]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 53
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40S ribosomal protein S14-ADB [auth DO]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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Entity ID: 54
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40S ribosomal protein S16-AEB [auth DQ]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 55
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40S ribosomal protein S18-AFB [auth DS]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 56
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40S ribosomal protein S19-AGB [auth DT]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 57
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40S ribosomal protein S22-AHB [auth DW]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 58
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40S ribosomal protein S23-AIB [auth DX]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 59
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40S ribosomal protein S24-AJB [auth DY]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 60
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40S ribosomal protein S28-AKB [auth Dc]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 65
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Exosome complex component RRP45PB [auth EB]305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
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Entity ID: 66
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Exosome complex component SKI6QB [auth EC]246Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6ECM20RRP41YGR195WG7587
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Entity ID: 67
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Exosome complex component RRP43RB [auth ED]394Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43YCR035CYCR35CYCR522
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Entity ID: 68
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Exosome complex component RRP46SB [auth EE]223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
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Entity ID: 69
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Exosome complex component RRP42TB [auth EF]265Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP42YDL111C
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Entity ID: 70
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Exosome complex component MTR3UB [auth EG]250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR3YGR158CG6676
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Entity ID: 71
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Exosome complex component RRP40VB [auth EH]240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
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Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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