6LQP

Cryo-EM structure of 90S small subunit preribosomes in transition states (State A)

  • Classification: RIBOSOME
  • Organism(s): Saccharomyces cerevisiae S288C
  • Mutation(s): No 

  • Deposited: 2020-01-14 Released: 2020-09-16 
  • Deposition Author(s): Du, Y., Ye, K.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.

Du, Y.An, W.Zhu, X.Sun, Q.Qi, J.Ye, K.

(2020) Science 369: 1477-1481

  • DOI: 10.1126/science.aba9690
  • Primary Citation of Related Structures:  
    6LQT, 6LQS, 6LQV, 6LQU, 6LQP, 6LQR, 6LQQ

  • PubMed Abstract: 
  • The 90 S preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 S ribosome. Here, we gained insight into this transition by determining cryo-electron microsco ...

    The 90 S preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 S ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of Saccharomyces cerevisiae intermediates in the path from the 90 S to the pre-40 S The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90 S , driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90 S through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90 S progression.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing 100049, China.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-ASC255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-ASF261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5SG225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-ASH236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-ASI190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 9
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40S ribosomal protein S8-ASJ200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 10
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40S ribosomal protein S9-ASK197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 11
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40S ribosomal protein S11-ASM156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 12
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40S ribosomal protein S12SN143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 13
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40S ribosomal protein S13SO151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 14
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40S ribosomal protein S14-ASP137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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Entity ID: 15
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40S ribosomal protein S16-ASR143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 16
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40S ribosomal protein S18-AST146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 17
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40S ribosomal protein S22-BSX130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22BRPS24BYLR367WL8039.6
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Entity ID: 18
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40S ribosomal protein S23-ASY145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 19
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40S ribosomal protein S24-ASZ135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 20
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40S ribosomal protein S27-ASc82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 21
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40S ribosomal protein S28-ASd67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarin3B3C327Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP1LOT3YDL014WD2870
EC: 2.1.1
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar protein 563D504Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP56SIK1YLR197WL8167.9
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Entity ID: 24
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Nucleolar protein 583E511Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP58NOP5YOR310CO6108
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Entity ID: 25
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Ribosomal RNA-processing protein 93F573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9YPR137W
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Entity ID: 26
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13 kDa ribonucleoprotein-associated protein3G3H126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 4A4776Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP4YDR324C
Find proteins for Q06679 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 5A5643Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP5YDR398WD9509.17
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 8A8713Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP8YGR128C
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 9A9575Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP9YHR196W
Find proteins for P38882 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 10AE1769Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP10YJL109CJ0808
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 15AF513Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP15YMR093WYM9582.18
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Entity ID: 33
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NET1-associated nuclear protein 1AG896Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAN1UTP17YPL126W
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Entity ID: 34
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Periodic tryptophan protein 2B1923Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2UTP1YCR057CYCR55C/YCR57C/YCR58C
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Entity ID: 35
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U3 small nucleolar RNA-associated protein 12B2943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2UTP12YLR129WL3116L9233.1
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 13B3817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13YLR222C
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18B8594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP18YJL069CHRE594J1098
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21BE939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21YLR409CL8084.22
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Entity ID: 39
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U3 small nucleolar RNA-associated protein 6B6440Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP6YDR449CD9461.34
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Entity ID: 40
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Bud site selection protein 215B214Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD21UTP16YOR078WYOR29-29
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Entity ID: 41
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U3 small nucleolar RNA-associated protein 75C554Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP7KRE31YER082C
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Entity ID: 42
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U3 small nucleolar RNA-associated protein 115D250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP11YKL099CYKL449
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Entity ID: 43
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U3 small nucleolar RNA-associated protein MPP105E593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10YJR002WJ1411YJR83.5
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Entity ID: 44
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U3 small nucleolar ribonucleoprotein protein IMP35F183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3YHR148W
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Entity ID: 45
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U3 small nucleolar ribonucleoprotein protein IMP45G290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4YNL075WN2353
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Entity ID: 46
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Something about silencing protein 105H610Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAS10UTP3YDL153CD1545
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Entity ID: 47
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Protein SOF15I489Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SOF1YLL011WL1339
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Entity ID: 48
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rRNA-processing protein FCF25J217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF2YLR051CL2128
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Entity ID: 49
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rRNA-processing protein FCF15K189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF1YDR339CD9651.9
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
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Ribosome biogenesis protein ENP2RA707Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP2YGR145WG6623
Find proteins for P48234 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
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U3 small nucleolar ribonucleoprotein protein LCP5RB357Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LCP5YER127WSYGP-ORF43
Find proteins for P40079 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
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KRR1 small subunit processome componentRC316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRR1YCL059CYCL59C
Find proteins for P25586 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 22RE1237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22YGR090W
Find proteins for P53254 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
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Ribosomal RNA-processing protein 7RF297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7YCL031CYCL184YCL31C
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Entity ID: 55
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Ribosomal RNA small subunit methyltransferase NEP1RGRH252Saccharomyces 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: 56
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Ribosome biogenesis protein UTP30RI274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP30YKR060W
Find proteins for P36144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
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Ribosome biogenesis protein BMS1RJ1183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1YPL217C
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Entity ID: 58
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RNA 3'-terminal phosphate cyclase-like proteinRK367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1RTC1YOL010W
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
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RNA cytidine acetyltransferaseRLRM1056Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRE33NAT10RRA1YNL132WN1216N1858
EC: 2.3.1
Find proteins for P53914 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
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Nucleolar complex protein 14RN810Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP14UTP2YDL148CD1566
Find proteins for Q99207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
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Nucleolar complex protein 4RO552Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOC4UTP19YPR144C
Find proteins for Q06512 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 62
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U3 small nucleolar RNA-associated protein 20RP2493Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP20YBL004WYBL0101
Find proteins for P35194 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
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U3 small nucleolar RNA-associated protein 14RQ899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP14YML093W
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Entity ID: 64
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Essential nuclear protein 1RS483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1MEG1YBR247CYBR1635
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Entity ID: 65
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Pno1RT326Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 66
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Protein FAF1RV346Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FAF1YIL019W
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Entity ID: 67
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Regulator of rDNA transcription protein 14RW206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRT14YIL127C
Find proteins for P40470 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
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Protein BFR2RY534Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BFR2YDR299W
Find proteins for Q06631 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
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Unassigned helicesX1347Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
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U3 snoRNA3A333Saccharomyces cerevisiae S288C
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Entity ID: 2
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5' ETS5A700Saccharomyces cerevisiae S288C
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Entity ID: 3
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18S pre-rRNASA1808Saccharomyces cerevisiae S288C
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
RJ
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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5K, Sc
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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RJ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-01-14 
  • Released Date: 2020-09-16 
  • Deposition Author(s): Du, Y., Ye, K.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91940302
Chinese Academy of SciencesChinaXDB08010203
National Natural Science Foundation of China (NSFC)China91540201
National Natural Science Foundation of China (NSFC)China31430024
National Natural Science Foundation of China (NSFC)China31325007

Revision History 

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references