5WYK

Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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

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
  • Structures With Same Primary Citation

  • 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 cere ...

    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 LengthOrganismDetails
rRNA 2'-O-methyltransferase fibrillarin3B, 3C327Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP1LOT3YDL014WD2870
EC: 2.1.1
Find proteins for P15646 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 563D504Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP56SIK1YLR197WL8167.9
Find proteins for Q12460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nucleolar protein 583E511Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP58NOP5YOR310CO6108
Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
13 kDa ribonucleoprotein-associated protein3G, 3H126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Utp4AA776Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Utp5AB643Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Utp9AD575Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 10AE1769Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP10YJL109CJ0808
Find proteins for P42945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Utp15AF513Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Utp17AG896Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein BMS1B11183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1YPL217C
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Periodic tryptophan protein 2BA923Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2UTP1YCR057CYCR55C/YCR57C/YCR58C
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 18BD594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP18YJL069CHRE594J1098
Find proteins for P40362 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 21BE939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21YLR409CL8084.22
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 7CA297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7YCL031CYCL184YCL31C
Find proteins for P25368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 22CB1237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22YGR090W
Find proteins for P53254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Enp2E4707Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
KRR1 small subunit processome componentK1316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRR1YCL059CYCL59C
Find proteins for P25586 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar ribonucleoprotein protein IMP3MA183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3YHR148W
Find proteins for P32899 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar ribonucleoprotein protein IMP4MB290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4YNL075WN2353
Find proteins for P53941 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Mpp10,U3 small nucleolar RNA-associated protein MPP10MC593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10
Find proteins for P47083 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Pre-rRNA-processing protein PNO1P1274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNO1DIM2RRP20YOR145CO3513YOR3513C
Find proteins for Q99216 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-ASC255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-ASF261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5SG225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-ASI190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-ASJ200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-ASM156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13SO151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-ASP137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-ASX130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-ASY145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-ASd67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
Utp7U1554Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Utp11U2250Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
rRNA-processing protein FCF1U4189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF1YDR339CD9651.9
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Ribosome biogenesis protein UTP30U5274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP30YKR060W
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
Helical domain proteinUB987Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Unassigned helicesUC1033Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Utp8AC713Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 12BB943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2UTP12YLR129WL3116L9233.1
Find proteins for Q12220 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
U3 small nucleolar RNA-associated protein 13BC817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13YLR222C
Find proteins for Q05946 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA small subunit methyltransferase NEP1E1, E2252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EMG1NEP1YLR186WL9470.5
EC: 2.1.1.260
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
RNA 3'-terminal phosphate cyclase-like proteinR1367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1RTC1YOL010W
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Sof1S1489Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-ASK197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-ASR143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-ASZ135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-ASc82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-ASf63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal RNA-processing protein 93F573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9YPR137W
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Helical domain proteinUA1615Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
U3 RNA3A333Saccharomyces cerevisiae S288C

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Entity ID: 32
MoleculeChainsLengthOrganism
18S ribosomal RNASA1812Saccharomyces cerevisiae S288C

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Entity ID: 7
MoleculeChainsLengthOrganism
5ETS RNA5A700Saccharomyces cerevisiae S288C
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Structure summary