6G4W

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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

Visualizing late states of human 40S ribosomal subunit maturation.

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

(2018) Nature 558: 249-253

  • DOI: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17B [auth R]135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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GTEx:  ENSG00000182774 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27C [auth b]84Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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GTEx:  ENSG00000177954 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aD [auth B]264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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GTEx:  ENSG00000145425 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28E [auth c]69Homo sapiensMutation(s): 0 
Gene Names: RPS28
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GTEx:  ENSG00000233927 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformF [auth E]263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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GTEx:  ENSG00000198034 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30G [auth e]59Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5H [auth F]204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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GTEx:  ENSG00000083845 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7I [auth H]194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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GTEx:  ENSG00000171863 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6J [auth G]249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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GTEx:  ENSG00000137154 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25K [auth Z]125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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GTEx:  ENSG00000118181 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24L [auth Y]133Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein PNO1M [auth x]252Homo sapiensMutation(s): 0 
Gene Names: PNO1
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GTEx:  ENSG00000115946 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23N [auth X]143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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GTEx:  ENSG00000186468 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
BystinO [auth w]437Homo sapiensMutation(s): 0 
Gene Names: BYSLENP1
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GTEx:  ENSG00000112578 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aP [auth W]130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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GTEx:  ENSG00000134419 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-rRNA-processing protein TSR1 homologQ [auth u]804Homo sapiensMutation(s): 0 
Gene Names: TSR1KIAA1401
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GTEx:  ENSG00000167721 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
UNKNOWNR [auth t]18Homo sapiensMutation(s): 0 
Gene Names: LTV1C6orf93
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GTEx:  ENSG00000135521 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19S [auth T]145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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GTEx:  ENSG00000105372 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18T [auth S]152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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GTEx:  ENSG00000231500 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16U [auth Q]146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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GTEx:  ENSG00000105193 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15V [auth P]145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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GTEx:  ENSG00000115268 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14W [auth O]151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13X [auth N]151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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GTEx:  ENSG00000110700 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11Y [auth L]158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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GTEx:  ENSG00000142534 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9Z [auth J]194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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GTEx:  ENSG00000170889 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8AA [auth I]208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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GTEx:  ENSG00000142937 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
RRP12BA [auth s]800Homo sapiensMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Multifunctional methyltransferase subunit TRM112-like proteinCA [auth r]125Homo sapiensMutation(s): 0 
Gene Names: TRMT112AD-001HSPC152HSPC170
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GTEx:  ENSG00000173113 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Probable 18S rRNA (guanine-N(7))-methyltransferaseDA [auth q]281Homo sapiensMutation(s): 0 
Gene Names: BUD23MERM1WBSCR22HUSSY-03PP3381
EC: 2.1.1
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GTEx:  ENSG00000071462 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
UNKNOWN HELIXEA [auth k]19Homo sapiensMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA [auth 2]1882Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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