6ZQC

Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Pre-A1


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

90 S pre-ribosome transformation into the primordial 40 S subunit.

Cheng, J.Lau, B.La Venuta, G.Ameismeier, M.Berninghausen, O.Hurt, E.Beckmann, R.

(2020) Science 369: 1470-1476

  • DOI: 10.1126/science.abb4119
  • Primary Citation of Related Structures:  
    6ZQF, 6ZQE, 6ZQG, 6ZQB, 6ZQA, 6ZQD, 6ZQC

  • PubMed Abstract: 
  • Production of small ribosomal subunits initially requires the formation of a 90 S precursor followed by an enigmatic process of restructuring into the primordial pre-40 S subunit. We elucidate this process by biochemical and cryo-elec ...

    Production of small ribosomal subunits initially requires the formation of a 90 S precursor followed by an enigmatic process of restructuring into the primordial pre-40 S subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 S pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A 1 , thereby separating the 5'-external transcribed spacer (ETS) from 18 S ribosomal RNA. Next, the 5'-ETS and 90 S assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 S emerges, still retaining some 90 S factors including Dhr1, now ready to unwind the final small nucleolar U3-18 S RNA hybrid. Our data shed light on the elusive 90 S to pre-40 S transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.


    Organizational Affiliation

    Gene Center, Department of Biochemistry, University of Munich, 81377 Munich, Germany. beckmann@genzentrum.lmu.de ed.hurt@bzh.uni-heidelberg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinCACB327Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP1LOT3YDL014WD2870
EC: 2.1.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-ADA255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA cytidine acetyltransferaseJAJB1056Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRE33NAT10RRA1YNL132WN1216N1858
EC: 2.3.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Periodic tryptophan protein 2UA923Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2UTP1YCR057CYCR55C/YCR57C/YCR58C
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar complex protein 14UB810Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP14UTP2YDL148CD1566
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Something about silencing protein 10UC610Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAS10UTP3YDL153CD1545
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Entity ID: 7
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U3 small nucleolar RNA-associated protein 4UD776Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP4YDR324C
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Entity ID: 8
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U3 small nucleolar RNA-associated protein 5UE643Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP5YDR398WD9509.17
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Entity ID: 9
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U3 small nucleolar RNA-associated protein 6UF440Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP6YDR449CD9461.34
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Entity ID: 10
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U3 small nucleolar RNA-associated protein 7UG554Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP7KRE31YER082C
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Entity ID: 11
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U3 small nucleolar RNA-associated protein 8UH713Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP8YGR128C
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Entity ID: 12
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U3 small nucleolar RNA-associated protein 9UI575Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP9YHR196W
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Entity ID: 13
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U3 small nucleolar RNA-associated protein 10UJ1769Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP10YJL109CJ0808
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Entity ID: 14
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U3 small nucleolar RNA-associated protein 11UK250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP11YKL099CYKL449
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Entity ID: 15
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U3 small nucleolar RNA-associated protein 12UL943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2UTP12YLR129WL3116L9233.1
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Entity ID: 16
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U3 small nucleolar RNA-associated protein 13UM817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13YLR222C
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Entity ID: 17
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U3 small nucleolar RNA-associated protein 14UN899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP14YML093W
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Entity ID: 18
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U3 small nucleolar RNA-associated protein 15UO513Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP15YMR093WYM9582.18
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Bud site selection protein 21UP214Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD21UTP16YOR078WYOR29-29
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
NET1-associated nuclear protein 1UQ896Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAN1UTP17YPL126W
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Entity ID: 21
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U3 small nucleolar RNA-associated protein 18UR594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP18YJL069CHRE594J1098
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar complex protein 4US552Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOC4UTP19YPR144C
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 20UT2493Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP20YBL004WYBL0101
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21UU939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21YLR409CL8084.22
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Entity ID: 25
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U3 small nucleolar RNA-associated protein 22UV1237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22YGR090W
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Entity ID: 26
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rRNA-processing protein FCF1UX189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF1YDR339CD9651.9
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein UTP30UZ274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP30YKR060W
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar protein 56CD504Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP56SIK1YLR197WL8167.9
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleolar protein 58CE511Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP58NOP5YOR310CO6108
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Entity ID: 30
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13 kDa ribonucleoprotein-associated proteinCFCG126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
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Entity ID: 31
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Ribosomal RNA-processing protein 9CH573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9YPR137W
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3CI183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3YHR148W
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Entity ID: 33
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U3 small nucleolar ribonucleoprotein protein IMP4CJ290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4YNL075WN2353
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Entity ID: 34
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U3 small nucleolar RNA-associated protein MPP10CK593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10YJR002WJ1411YJR83.5
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1CL1183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1YPL217C
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinCM367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1RTC1YOL010W
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Entity ID: 37
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Ribosomal RNA-processing protein 7CN297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7YCL031CYCL184YCL31C
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Entity ID: 38
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Ribosome biogenesis protein ENP2JC707Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP2YGR145WG6623
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Entity ID: 39
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Ribosomal RNA small subunit methyltransferase NEP1JFJG252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EMG1NEP1YLR186WL9470.5
EC: 2.1.1.260
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Essential nuclear protein 1JH483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1MEG1YBR247CYBR1635
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Entity ID: 41
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rRNA biogenesis protein RRP5JI1729Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP5FMI1YMR229CYM9959.11C
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Entity ID: 42
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Pre-rRNA-processing protein PNO1JJ274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNO1DIM2RRP20YOR145CO3513YOR3513C
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Entity ID: 43
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Protein BFR2JK534Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BFR2YDR299W
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Entity ID: 44
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rRNA-processing protein FCF2JM217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF2YLR051CL2128
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Entity ID: 45
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Protein FAF1JN346Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FAF1YIL019W
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Entity ID: 46
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KRR1 small subunit processome componentJO316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRR1YCL059CYCL59C
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Entity ID: 47
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Protein SOF1JP489Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SOF1YLL011WL1339
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Entity ID: 48
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Regulator of rDNA transcription protein 14JQ206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRT14YIL127C
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Entity ID: 49
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40S ribosomal protein S4-ADE261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5DF225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
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40S ribosomal protein S6-ADG236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 52
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40S ribosomal protein S7-ADH190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
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40S ribosomal protein S8-ADI200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 54
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40S ribosomal protein S9-ADJ197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
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40S ribosomal protein S11-ADL156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
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40S ribosomal protein S13DN151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
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40S ribosomal protein S14-ADO137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
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40S ribosomal protein S16-ADQ143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
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40S ribosomal protein S18-ADS146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 60
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40S ribosomal protein S22-ADW130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
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40S ribosomal protein S23-ADX145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 62
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40S ribosomal protein S24-ADY135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 63
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40S ribosomal protein S27-ADb82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
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40S ribosomal protein S28-ADc67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
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5ETS RNAD2700Saccharomyces cerevisiae S288C
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Entity ID: 66
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18S rRNAD31808Saccharomyces cerevisiae S288C
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Entity ID: 67
MoleculeChainsLengthOrganismImage
U3 snoRNAD4333Saccharomyces cerevisiae S288C
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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

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Db, UX
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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CL, UX
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references