5WYJ

Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 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

Molecular architecture of the 90S small subunit pre-ribosome.

Sun, Q.Zhu, X.Qi, J.An, W.Lan, P.Tan, D.Chen, R.Wang, B.Zheng, S.Zhang, C.Chen, X.Zhang, W.Chen, J.Dong, M.Q.Ye, K.

(2017) Elife 6

  • DOI: 10.7554/eLife.22086
  • Primary Citation of Related Structures:  
    5WWN, 5WWO, 5WY3, 5WXM, 5WXL, 5WYJ, 5WYL, 5WYK

  • PubMed Abstract: 
  • Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4 ...

    Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, China.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinB [auth 3B], C [auth 3C]327Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP1LOT3YDL014WD2870
EC: 2.1.1
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Entity ID: 3
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Nucleolar protein 56D [auth 3D]504Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP56SIK1YLR197WL8167.9
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Entity ID: 4
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Nucleolar protein 58E [auth 3E]511Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP58NOP5YOR310CO6108
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Entity ID: 5
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Ribosomal RNA-processing protein 9F [auth 3F]573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9YPR137W
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Entity ID: 6
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13 kDa ribonucleoprotein-associated proteinG [auth 3G], H [auth 3H]126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
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Entity ID: 8
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Utp4J [auth AA]776Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
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Utp5K [auth AB]643Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
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Utp8L [auth AC]713Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
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Utp9M [auth AD]575Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
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U3 small nucleolar RNA-associated protein 10,Utp10N [auth AE]1769Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP10
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Entity ID: 13
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Utp15O [auth AF]513Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
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Utp17P [auth AG]896Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
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Ribosome biogenesis protein BMS1Q [auth B1]1183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1YPL217C
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Entity ID: 16
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Periodic tryptophan protein 2R [auth BA]923Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2UTP1YCR057CYCR55C/YCR57C/YCR58C
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Entity ID: 17
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U3 small nucleolar RNA-associated protein 12S [auth BB]943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2UTP12YLR129WL3116L9233.1
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Entity ID: 18
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U3 small nucleolar RNA-associated protein 13T [auth BC]817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13YLR222C
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Entity ID: 19
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U3 small nucleolar RNA-associated protein 18U [auth BD]594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP18YJL069CHRE594J1098
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Entity ID: 20
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U3 small nucleolar RNA-associated protein 21V [auth BE]939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21YLR409CL8084.22
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Entity ID: 21
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Ribosomal RNA-processing protein 7W [auth CA]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7YCL031CYCL184YCL31C
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Entity ID: 22
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U3 small nucleolar RNA-associated protein 22X [auth CB]1237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22YGR090W
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Entity ID: 23
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Ribosomal RNA small subunit methyltransferase NEP1Y [auth E1], Z [auth E2]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EMG1NEP1YLR186WL9470.5
EC: 2.1.1.260
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Entity ID: 24
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Essential nuclear protein 1AA [auth E3]483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1MEG1YBR247CYBR1635
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Entity ID: 25
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Enp2BA [auth E4]707Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
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KRR1 small subunit processome componentCA [auth K1]316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRR1YCL059CYCL59C
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Entity ID: 27
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U3 small nucleolar ribonucleoprotein protein IMP3DA [auth MA]183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3YHR148W
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Entity ID: 28
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U3 small nucleolar ribonucleoprotein protein IMP4EA [auth MB]290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4YNL075WN2353
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Entity ID: 29
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Mpp10,U3 small nucleolar RNA-associated protein MPP10FA [auth MC]593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10
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Entity ID: 30
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Pre-rRNA-processing protein PNO1GA [auth P1]274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNO1DIM2RRP20YOR145CO3513YOR3513C
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Entity ID: 31
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RNA 3'-terminal phosphate cyclase-like proteinHA [auth R1]367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1RTC1YOL010W
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Entity ID: 32
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rRNA biogenesis protein RRP5IA [auth R2]1729Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP5FMI1YMR229CYM9959.11C
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Entity ID: 33
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Sof1JA [auth S1]489Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
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40S ribosomal protein S1-ALA [auth SC]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 36
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40S ribosomal protein S4-AMA [auth SF]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 37
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40S ribosomal protein S5NA [auth SG]225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 38
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40S ribosomal protein S6-AOA [auth SH]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 39
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40S ribosomal protein S7-APA [auth SI]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 40
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40S ribosomal protein S8-AQA [auth SJ]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 41
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40S ribosomal protein S9-ARA [auth SK]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 42
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40S ribosomal protein S11-ASA [auth SM]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 43
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40S ribosomal protein S12TA [auth SN]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 44
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40S ribosomal protein S13UA [auth SO]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 45
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40S ribosomal protein S14-AVA [auth SP]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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40S ribosomal protein S16-AWA [auth SR]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 47
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40S ribosomal protein S22-AXA [auth SX]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 48
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40S ribosomal protein S23-AYA [auth SY]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 49
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40S ribosomal protein S24-AZA [auth SZ]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 50
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40S ribosomal protein S27-AAB [auth Sc]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 51
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40S ribosomal protein S28-ABB [auth Sd]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 52
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40S ribosomal protein S30-ACB [auth Sf]63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
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Entity ID: 53
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Ubiquitin-40S ribosomal protein S31DB [auth Sg]152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
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Entity ID: 54
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Utp7EB [auth U1]554Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 55
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Utp11FB [auth U2]250Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 56
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Utp20GB [auth U3]2493Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 57
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rRNA-processing protein FCF1HB [auth U4]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF1YDR339CD9651.9
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Entity ID: 58
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Ribosome biogenesis protein UTP30IB [auth U5]274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP30YKR060W
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Entity ID: 59
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Helical domain proteinJB [auth UA]1615Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
Helical domain proteinKB [auth UB]987Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned helicesLB [auth UC]1033Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U3 RNAA [auth 3A]333Saccharomyces cerevisiae S288C
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Entity ID: 7
MoleculeChainsLengthOrganismImage
5ETS RNAI [auth 5A]700Saccharomyces cerevisiae S288C
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Entity ID: 34
MoleculeChainsLengthOrganismImage
18S ribosomal RNAKA [auth SA]1812Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2017-01-13 
  • Released Date: 2017-03-29 
  • Deposition Author(s): Ye, K., Zhu, X., Sun, Q.

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Structure summary
  • Version 1.2: 2019-10-09
    Changes: Data collection, Other