7WTS

Cryo-EM structure of a human pre-40S ribosomal subunit - State UTP14


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 1.2 of the entry. See complete history


Literature

The nucleoplasmic phase of pre-40S formation prior to nuclear export.

Cheng, J.Lau, B.Thoms, M.Ameismeier, M.Berninghausen, O.Hurt, E.Beckmann, R.

(2022) Nucleic Acids Res 50: 11924-11937

  • DOI: https://doi.org/10.1093/nar/gkac961
  • Primary Citation of Related Structures:  
    7WTN, 7WTO, 7WTP, 7WTQ, 7WTR, 7WTS, 7WTT, 7WTU, 7WTV, 7WTW, 7WTX, 7WTZ, 7WU0

  • PubMed Abstract: 

    Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.


  • Organizational Affiliation

    Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Dong'an Road 131, 200032 Shanghai, China.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27B [auth b]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aC [auth B]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformD [auth E]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30E [auth e]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7F [auth H]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24H [auth Y]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein PNO1I [auth x]252Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115946 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23J [auth X]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aK [auth W]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein TSR1 homologL [auth u]804Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167721 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14M [auth O]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11O [auth L]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9P [auth J]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8Q [auth I]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Multifunctional methyltransferase subunit TRM112-like proteinR [auth r]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173113 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Probable 18S rRNA (guanine-N(7))-methyltransferaseS [auth q]281Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000071462 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RRP12-like proteinT [auth K]1,297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000052749 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein SLX9 homologU [auth z]230Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000160256 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 14 homolog AV [auth 5]771Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156697 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Probable dimethyladenosine transferaseW [auth 3]313Homo sapiensMutation(s): 0 
EC: 2.1.1.183
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PHAROS:  Q9UNQ2
GTEx:  ENSG00000086189 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth 2]1,873Homo sapiens
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Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2022-12-21
    Changes: Database references