6G4S

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Visualizing late states of human 40S ribosomal subunit maturation.

Ameismeier, M.Cheng, J.Berninghausen, O.Beckmann, R.

(2018) Nature 558: 249-253

  • DOI: https://doi.org/10.1038/s41586-018-0193-0
  • Primary Citation of Related Structures:  
    6G18, 6G4S, 6G4W, 6G51, 6G53, 6G5H, 6G5I

  • PubMed Abstract: 

    The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage.


  • Organizational Affiliation

    Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.


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 SAC [auth A]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27D [auth b]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aE [auth B]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2F [auth C]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28G [auth c]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformH [auth E]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30I [auth e]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5J [auth F]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7K [auth H]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6L [auth G]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25M [auth Z]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24N [auth Y]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein NOB1O [auth y]412Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141101 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein PNO1P [auth x]252Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115946 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23Q [auth X]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
BystinR [auth w]437Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112578 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aS [auth W]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21T [auth V]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-rRNA-processing protein TSR1 homologU [auth u]804Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167721 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LTV1 homologV [auth t]475Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135521 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19W [auth T]145Homo sapiensMutation(s): 0 
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Find proteins for P39019 (Homo sapiens)
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GTEx:  ENSG00000105372 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18X [auth S]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16Y [auth Q]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15Z [auth P]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14AA [auth O]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13BA [auth N]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11CA [auth L]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9DA [auth J]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8EA [auth I]208Homo sapiensMutation(s): 0 
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Find proteins for P62241 (Homo sapiens)
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GTEx:  ENSG00000142937 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RRP12FA [auth s]800Homo sapiensMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
UnknownGA [auth k]39Homo sapiensMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
pre-18S ribosomal RNAA [auth 2]1,882Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB646
German Research FoundationGermanyGRK1721
German Research FoundationGermanyFOR1805
European Research CouncilGermanyCRYOTRANSLATION

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Other