6G53

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


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 1.5 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, 6G5I, 6G5H

  • 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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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAC [auth A]295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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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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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2E [auth C]293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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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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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6G249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7H194Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8I208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9J194Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11K [auth L]158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13L [auth N]151Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14M [auth O]151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21N [auth V]83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aO [auth W]130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23P [auth X]143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24Q [auth Y]133Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27R [auth b]84Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30S [auth e]59Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein PNO1T [auth x]252Homo sapiensMutation(s): 0 
Gene Names: PNO1
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein NOB1U [auth y]412Homo sapiensMutation(s): 0 
Gene Names: NOB1ART4NOB1PPSMD8BP1MSTP158
EC: 3.1
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-rRNA-processing protein TSR1 homologV [auth u]804Homo sapiensMutation(s): 0 
Gene Names: TSR1KIAA1401
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LTV1 homologW [auth t]475Homo sapiensMutation(s): 0 
Gene Names: LTV1C6orf93
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29X [auth d]56Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3Y [auth D]243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5Z [auth F]204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10AA [auth K]165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12BA [auth M]132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15CA [auth P]145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16DA [auth Q]146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18EA [auth S]152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19FA [auth T]145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20GA [auth U]119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 34
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40S ribosomal protein S25HA [auth Z]125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28IA [auth c]69Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aJA [auth f]156Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1KA [auth g]317Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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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
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-12-11
    Changes: Other