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 ...

    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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAA295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
Find proteins for P08865 (Homo sapiens)
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PHAROS  P08865
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8I208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
Find proteins for P62241 (Homo sapiens)
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PHAROS  P62241
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13N151Homo sapiensMutation(s): 0 
Gene Names: RPS13
Find proteins for P62277 (Homo sapiens)
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PHAROS  P62277
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21V83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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PHAROS  P63220
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein PNO1x252Homo sapiensMutation(s): 0 
Gene Names: PNO1
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PHAROS  Q9NRX1
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein NOB1y412Homo sapiensMutation(s): 0 
Gene Names: NOB1ART4NOB1PPSMD8BP1MSTP158
EC: 3.1
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PHAROS  Q9ULX3
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Pre-rRNA-processing protein TSR1 homologu804Homo sapiensMutation(s): 0 
Gene Names: TSR1KIAA1401
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PHAROS  Q2NL82
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3D243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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PHAROS  P23396
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19T145Homo sapiensMutation(s): 0 
Gene Names: RPS19
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PHAROS  P39019
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20U119Homo sapiensMutation(s): 0 
Gene Names: RPS20
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PHAROS  P60866
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28c69Homo sapiensMutation(s): 0 
Gene Names: RPS28
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PHAROS  P62857
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1g317Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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PHAROS  P63244
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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 S11L158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14O151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aW130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23X143Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24Y133Homo sapiensMutation(s): 0 
Gene Names: RPS24
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PHAROS  P62847
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27b84Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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PHAROS  P42677
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30e59Homo sapiensMutation(s): 0 
Gene Names: FAU
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PHAROS  P62861
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17R135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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PHAROS  P08708
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Protein LTV1 homologt475Homo sapiensMutation(s): 0 
Gene Names: LTV1C6orf93
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PHAROS  Q96GA3
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29d56Homo sapiensMutation(s): 0 
Gene Names: RPS29
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PHAROS  P62273
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5F204Homo sapiensMutation(s): 0 
Gene Names: RPS5
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PHAROS  P46782
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10K165Homo sapiensMutation(s): 0 
Gene Names: RPS10
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PHAROS  P46783
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12M132Homo sapiensMutation(s): 0 
Gene Names: RPS12
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PHAROS  P25398
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15P145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16Q146Homo sapiensMutation(s): 0 
Gene Names: RPS16
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PHAROS  P62249
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18S152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25Z125Homo sapiensMutation(s): 0 
Gene Names: RPS25
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PHAROS  P62851
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27af156Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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PHAROS  P62979
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3aB264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2C293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformE263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
Find proteins for P62701 (Homo sapiens)
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PHAROS  P62701
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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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PHAROS  P62753
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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: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNA21882Homo sapiens
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 

  • 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