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: https://doi.org/10.7554/eLife.22086
  • Primary Citation of Related Structures:  
    5WWN, 5WWO, 5WXL, 5WXM, 5WY3, 5WYJ, 5WYK, 5WYL

  • 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 4.5 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

    PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA 2'-O-methyltransferase fibrillarinB [auth 3B],
C [auth 3C]
327Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 56D [auth 3D]504Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar protein 58E [auth 3E]511Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 9F [auth 3F]573Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
13 kDa ribonucleoprotein-associated proteinG [auth 3G],
H [auth 3H]
126Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Utp4J [auth AA]776Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Utp5K [auth AB]643Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Utp8L [auth AC]713Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Utp9M [auth AD]575Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 10,Utp10N [auth AE]1,769Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Utp15O [auth AF]513Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Utp17P [auth AG]896Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein BMS1Q [auth B1]1,183Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Periodic tryptophan protein 2R [auth BA]923Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 12S [auth BB]943Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 13T [auth BC]817Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 18U [auth BD]594Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 21V [auth BE]939Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA-processing protein 7W [auth CA]297Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 22X [auth CB]1,237Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal RNA small subunit methyltransferase NEP1Y [auth E1],
Z [auth E2]
252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.1.1.260
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Essential nuclear protein 1AA [auth E3]483Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Enp2BA [auth E4]707Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
KRR1 small subunit processome componentCA [auth K1]316Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP3DA [auth MA]183Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar ribonucleoprotein protein IMP4EA [auth MB]290Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Mpp10,U3 small nucleolar RNA-associated protein MPP10FA [auth MC]593Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein PNO1GA [auth P1]274Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 3'-terminal phosphate cyclase-like proteinHA [auth R1]367Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA biogenesis protein RRP5IA [auth R2]1,729Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Sof1JA [auth S1]489Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-ALA [auth SC]255Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AMA [auth SF]261Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5NA [auth SG]225Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AOA [auth SH]236Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-APA [auth SI]190Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AQA [auth SJ]200Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-ARA [auth SK]197Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-ASA [auth SM]156Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12TA [auth SN]143Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13UA [auth SO]151Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AVA [auth SP]137Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AWA [auth SR]143Saccharomyces cerevisiae S288CMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AXA [auth SX]130Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AYA [auth SY]145Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AZA [auth SZ]135Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AAB [auth Sc]82Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-ABB [auth Sd]67Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-ACB [auth Sf]63Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP0CX33
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31DB [auth Sg]152Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Utp7EB [auth U1]554Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Utp11FB [auth U2]250Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Utp20GB [auth U3]2,493Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA-processing protein FCF1HB [auth U4]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q05498 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein UTP30IB [auth U5]274Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P36144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Helical domain proteinJB [auth UA]1,615Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Helical domain proteinKB [auth UB]987Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned helicesLB [auth UC]1,033Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
U3 RNAA [auth 3A]333Saccharomyces cerevisiae S288C
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Entity ID: 7
MoleculeChains LengthOrganismImage
5ETS RNAI [auth 5A]700Saccharomyces cerevisiae S288C
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Entity ID: 34
MoleculeChains LengthOrganismImage
18S ribosomal RNAKA [auth SA]1,812Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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