7WTZ

Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-B2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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 S5B [auth F]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12C [auth M]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15D [auth P]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16E [auth Q]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17F [auth R]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18G [auth S]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19H [auth T]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25I [auth Z]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28J [auth c]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aK [auth f]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAL [auth A]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aM [auth B]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2N [auth C]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformO [auth E]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6P [auth G]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7Q [auth H]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8R [auth I]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9S [auth J]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11T [auth L]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13U [auth N]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14V [auth O]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21W [auth V]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aX [auth W]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23Y [auth X]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24Z [auth Y]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27AA [auth b]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30BA [auth e]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein PNO1CA [auth x]252Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115946 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein NOB1DA [auth y]412Homo sapiensMutation(s): 0 
EC: 3.1
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GTEx:  ENSG00000141101 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein TSR1 homologEA [auth u]804Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167721 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
BystinFA [auth w]437Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112578 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LTV1 homologGA [auth t]475Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135521 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
RRP12-like proteinHA [auth K]1,297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000052749 
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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: 3.00 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