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 fibrillarin 3B, 3C327Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP1, LOT3, YDL014W, D2870
EC: 2.1.1
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Entity ID: 3
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Nucleolar protein 56 3D504Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP56, SIK1, YLR197W, L8167.9
Find proteins for Q12460 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
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Nucleolar protein 58 3E511Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP58, NOP5, YOR310C, O6108
Find proteins for Q12499 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9 3F573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9, YPR137W
Find proteins for Q06506 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated protein 3G, 3H126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13, YEL026W
Find proteins for P39990 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Utp4 AA776Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
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Utp5 AB643Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
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Utp8 AC713Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
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Utp9 AD575Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
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U3 small nucleolar RNA-associated protein 10,Utp10 AE1769Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP10
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Entity ID: 13
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Utp15 AF513Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
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Utp17 AG896Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
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Ribosome biogenesis protein BMS1 B11183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1, YPL217C
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Periodic tryptophan protein 2 BA923Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2, UTP1, YCR057C, YCR55C/YCR57C/YCR58C
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Entity ID: 17
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U3 small nucleolar RNA-associated protein 12 BB943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2, UTP12, YLR129W, L3116, L9233.1
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Entity ID: 18
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U3 small nucleolar RNA-associated protein 13 BC817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13, YLR222C
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Entity ID: 19
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U3 small nucleolar RNA-associated protein 18 BD594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP18, YJL069C, HRE594, J1098
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Entity ID: 20
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U3 small nucleolar RNA-associated protein 21 BE939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21, YLR409C, L8084.22
Find proteins for Q06078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
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Ribosomal RNA-processing protein 7 CA297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7, YCL031C, YCL184, YCL31C
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Entity ID: 22
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U3 small nucleolar RNA-associated protein 22 CB1237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22, YGR090W
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Entity ID: 23
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Ribosomal RNA small subunit methyltransferase NEP1 E1, E2252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EMG1, NEP1, YLR186W, L9470.5
EC: 2.1.1.260
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
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Essential nuclear protein 1 E3483Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1, MEG1, YBR247C, YBR1635
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Entity ID: 25
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Enp2 E4707Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
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KRR1 small subunit processome component K1316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KRR1, YCL059C, YCL59C
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3 MA183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3, YHR148W
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Entity ID: 28
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U3 small nucleolar ribonucleoprotein protein IMP4 MB290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4, YNL075W, N2353
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Entity ID: 29
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Mpp10,U3 small nucleolar RNA-associated protein MPP10 MC593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10
Find proteins for P47083 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
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Pre-rRNA-processing protein PNO1 P1274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PNO1, DIM2, RRP20, YOR145C, O3513, YOR3513C
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like protein R1367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1, RTC1, YOL010W
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA biogenesis protein RRP5 R21729Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP5, FMI1, YMR229C, YM9959.11C
Find proteins for Q05022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
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Sof1 S1489Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-A SC255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1A, PLC1, RPS10A, YLR441C, L9753.9
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-A SF261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4A, RPS7B, YJR145C, J2186
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5 SG225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5, RPS2, YJR123W, J2045
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 38
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40S ribosomal protein S6-A SH236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6A, RPS101, RPS10B, YPL090C, LPG18C
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Entity ID: 39
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40S ribosomal protein S7-A SI190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7A, RPS30, YOR096W, YOR3177W
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Entity ID: 40
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40S ribosomal protein S8-A SJ200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8A, RPS14A, YBL072C, YBL06.05, YBL0613
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Entity ID: 41
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40S ribosomal protein S9-A SK197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9A, RPS13A, YS11A, YPL081W
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Entity ID: 42
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40S ribosomal protein S11-A SM156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11A, RPS18A, YDR025W, YD9813.03
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Entity ID: 43
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40S ribosomal protein S12 SN143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12, YOR369C
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Entity ID: 44
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40S ribosomal protein S13 SO151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13, RPS13C, YDR064W, D4252, YD9609.18
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Entity ID: 45
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40S ribosomal protein S14-A SP137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14A, CRY1, RPL59, YCR031C, YCR31C
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Entity ID: 46
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40S ribosomal protein S16-A SR143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16A, RP61R, YMR143W, YM9375.12
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Entity ID: 47
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40S ribosomal protein S22-A SX130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22A, RPS24, RPS24A, YJL190C, J0355
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Entity ID: 48
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40S ribosomal protein S23-A SY145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23A, RPS28A, YGR118W, G6178
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Entity ID: 49
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40S ribosomal protein S24-A SZ135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24A, RPS24EA, YER074W
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Entity ID: 50
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40S ribosomal protein S27-A Sc82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27A, YKL156W
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Entity ID: 51
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40S ribosomal protein S28-A Sd67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28A, RPS33, RPS33A, YOR167C, O3600
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Entity ID: 52
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40S ribosomal protein S30-A Sf63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30A, YLR287C-A, L8003.23, YLR287BC
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Entity ID: 53
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Ubiquitin-40S ribosomal protein S31 Sg152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31, RPS37, UBI3, YLR167W, L9470.14
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Entity ID: 54
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Utp7 U1554Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 55
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Utp11 U2250Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 56
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Utp20 U32493Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 57
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rRNA-processing protein FCF1 U4189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF1, YDR339C, D9651.9
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
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Ribosome biogenesis protein UTP30 U5274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP30, YKR060W
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Entity ID: 59
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Helical domain protein UA1615Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 60
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Helical domain protein UB987Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 61
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Unassigned helices UC1033Saccharomyces cerevisiae S288CMutation(s): 0 
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U3 RNA3A333Saccharomyces cerevisiae S288C
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Entity ID: 7
MoleculeChainsLengthOrganismImage
5ETS RNA5A700Saccharomyces cerevisiae S288C
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Entity ID: 34
MoleculeChainsLengthOrganismImage
18S ribosomal RNASA1812Saccharomyces cerevisiae S288C
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


View more in-depth experimental data

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