7WTT

Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 S17B [auth R]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27C [auth b]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aD [auth B]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28E [auth c]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformF [auth E]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30G [auth e]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5H [auth F]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7I [auth H]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6J [auth G]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25K [auth Z]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24L [auth Y]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein PNO1M [auth x]252Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115946 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23N [auth X]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
BystinO [auth w]437Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112578 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aP [auth W]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein TSR1 homologQ [auth u]804Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167721 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LTV1 homologR [auth t]475Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135521 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19S [auth T]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18T [auth S]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16U [auth Q]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15V [auth P]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14W [auth O]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13X [auth N]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11Y [auth L]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9Z [auth J]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8AA [auth I]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Multifunctional methyltransferase subunit TRM112-like proteinBA [auth r]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173113 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Probable 18S rRNA (guanine-N(7))-methyltransferaseCA [auth q]281Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000071462 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RRP12-like proteinDA [auth K]1,297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000052749 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12EA [auth M]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aFA [auth f]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase I isoform alphaGA [auth a]337Homo sapiensMutation(s): 0 
EC: 2.7.11.1
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GTEx:  ENSG00000113712 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein SLX9 homologHA [auth z]230Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000160256 
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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: 3.10 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