6LQQ

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

  • 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: 4.10 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 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 ...

    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-AD [auth SC]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 5
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40S ribosomal protein S4-AE [auth SF]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 6
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40S ribosomal protein S5F [auth SG]225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 7
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40S ribosomal protein S6-AG [auth SH]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 8
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40S ribosomal protein S7-AH [auth SI]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 9
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40S ribosomal protein S8-AI [auth SJ]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 10
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40S ribosomal protein S9-AJ [auth SK]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 11
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40S ribosomal protein S11-AK [auth SM]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 12
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40S ribosomal protein S13L [auth SO]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 13
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40S ribosomal protein S14-AM [auth SP]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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Entity ID: 14
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40S ribosomal protein S16-AN [auth SR]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 15
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40S ribosomal protein S22-BO [auth SX]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22BRPS24BYLR367WL8039.6
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Entity ID: 16
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40S ribosomal protein S23-AP [auth SY]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 17
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40S ribosomal protein S24-AQ [auth SZ]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 18
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40S ribosomal protein S27-AR [auth Sc]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 19
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40S ribosomal protein S28-AS [auth Sd]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 20
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rRNA 2'-O-methyltransferase fibrillarinT [auth 3B], U [auth 3C]327Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP1LOT3YDL014WD2870
EC: 2.1.1
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Entity ID: 21
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Nucleolar protein 56V [auth 3D]504Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP56SIK1YLR197WL8167.9
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Entity ID: 22
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Nucleolar protein 58W [auth 3E]511Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP58NOP5YOR310CO6108
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Entity ID: 23
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Ribosomal RNA-processing protein 9X [auth 3F]573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9YPR137W
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Entity ID: 24
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13 kDa ribonucleoprotein-associated proteinY [auth 3G], Z [auth 3H]126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
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Entity ID: 25
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U3 small nucleolar RNA-associated protein 4AA [auth A4]776Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP4YDR324C
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Entity ID: 26
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U3 small nucleolar RNA-associated protein 5BA [auth A5]643Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP5YDR398WD9509.17
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Entity ID: 27
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U3 small nucleolar RNA-associated protein 8CA [auth A8]713Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP8YGR128C
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Entity ID: 28
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U3 small nucleolar RNA-associated protein 9DA [auth A9]575Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP9YHR196W
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Entity ID: 29
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U3 small nucleolar RNA-associated protein 10EA [auth AE]1769Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP10YJL109CJ0808
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Entity ID: 30
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U3 small nucleolar RNA-associated protein 15FA [auth AF]513Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP15YMR093WYM9582.18
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Entity ID: 31
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NET1-associated nuclear protein 1GA [auth AG]896Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAN1UTP17YPL126W
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Periodic tryptophan protein 2HA [auth B1]923Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2UTP1YCR057CYCR55C/YCR57C/YCR58C
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Entity ID: 33
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U3 small nucleolar RNA-associated protein 12IA [auth B2]943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2UTP12YLR129WL3116L9233.1
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Entity ID: 34
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U3 small nucleolar RNA-associated protein 13JA [auth B3]817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13YLR222C
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Entity ID: 35
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U3 small nucleolar RNA-associated protein 18KA [auth B8]594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP18YJL069CHRE594J1098
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Entity ID: 36
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U3 small nucleolar RNA-associated protein 21LA [auth BE]939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21YLR409CL8084.22
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Entity ID: 37
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U3 small nucleolar RNA-associated protein 6MA [auth B6]440Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP6YDR449CD9461.34
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Bud site selection protein 21NA [auth 5B]214Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD21UTP16YOR078WYOR29-29
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Find proteins for Q08492 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 7OA [auth 5C]554Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP7KRE31YER082C
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Entity ID: 40
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U3 small nucleolar RNA-associated protein 11PA [auth 5D]250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP11YKL099CYKL449
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Entity ID: 41
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U3 small nucleolar RNA-associated protein MPP10QA [auth 5E]593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10YJR002WJ1411YJR83.5
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Entity ID: 42
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U3 small nucleolar ribonucleoprotein protein IMP3RA [auth 5F]183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3YHR148W
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Entity ID: 43
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U3 small nucleolar ribonucleoprotein protein IMP4SA [auth 5G]290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4YNL075WN2353
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Entity ID: 44
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Something about silencing protein 10TA [auth 5H]610Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAS10UTP3YDL153CD1545
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Entity ID: 45
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Protein SOF1UA [auth 5I]489Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SOF1YLL011WL1339
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Entity ID: 46
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rRNA-processing protein FCF2VA [auth 5J]217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF2YLR051CL2128
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Entity ID: 47
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rRNA-processing protein FCF1WA [auth 5K]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF1YDR339CD9651.9
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Entity ID: 48
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Ribosome biogenesis protein ENP2XA [auth RA]707Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP2YGR145WG6623
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Entity ID: 49
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U3 small nucleolar ribonucleoprotein protein LCP5YA [auth RB]357Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LCP5YER127WSYGP-ORF43
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Entity ID: 50
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KRR1 small subunit processome componentZA [auth RC]316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRR1YCL059CYCL59C
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Entity ID: 51
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rRNA biogenesis protein RRP5AB [auth RD]1729Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP5FMI1YMR229CYM9959.11C
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Entity ID: 52
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U3 small nucleolar RNA-associated protein 22BB [auth RE]1237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22YGR090W
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Entity ID: 53
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Ribosomal RNA-processing protein 7CB [auth RF]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7YCL031CYCL184YCL31C
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1DB [auth RG], EB [auth RH]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EMG1NEP1YLR186WL9470.5
EC: 2.1.1.260
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1FB [auth RJ]1183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1YPL217C
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Entity ID: 56
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RNA 3'-terminal phosphate cyclase-like proteinGB [auth RK]367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1RTC1YOL010W
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
RNA cytidine acetyltransferaseHB [auth RL], IB [auth RM]1056Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRE33NAT10RRA1YNL132WN1216N1858
EC: 2.3.1
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar complex protein 14JB [auth RN]810Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP14UTP2YDL148CD1566
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar complex protein 4KB [auth RO]552Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOC4UTP19YPR144C
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20LB [auth RP]2493Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP20YBL004WYBL0101
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Entity ID: 61
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U3 small nucleolar RNA-associated protein 14MB [auth RQ]899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP14YML093W
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Entity ID: 62
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Essential nuclear protein 1NB [auth RS]483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1MEG1YBR247CYBR1635
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Entity ID: 63
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Pno1OB [auth RT]326Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 64
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Protein FAF1PB [auth RV]346Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FAF1YIL019W
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Entity ID: 65
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Protein BFR2QB [auth RY]534Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BFR2YDR299W
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned helicesRB [auth X1]347Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U3 snoRNAA [auth 3A]333Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5' ETSB [auth 5A]700Saccharomyces cerevisiae S288C
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Entity ID: 3
MoleculeChainsLengthOrganismImage
18S pre-rRNAC [auth SA]1808Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
UB [auth RJ]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
SB [auth Sc], TB [auth 5K]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
VB [auth RJ]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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, 91540201, 31430024, 31325007
Chinese Academy of SciencesChinaXDB08010203

Revision History  (Full details and data files)

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