7ZS5

Structure of 60S ribosomal subunit from S. cerevisiae with eIF6 and tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for clearing of ribosome collisions by the RQT complex.

Best, K.Ikeuchi, K.Kater, L.Best, D.Musial, J.Matsuo, Y.Berninghausen, O.Becker, T.Inada, T.Beckmann, R.

(2023) Nat Commun 14: 921-921

  • DOI: https://doi.org/10.1038/s41467-023-36230-8
  • Primary Citation of Related Structures:  
    7ZPQ, 7ZRS, 7ZS5, 7ZUW, 7ZUX

  • PubMed Abstract: 

    Translation of aberrant messenger RNAs can cause stalling of ribosomes resulting in ribosomal collisions. Collided ribosomes are specifically recognized to initiate stress responses and quality control pathways. Ribosome-associated quality control facilitates the degradation of incomplete translation products and requires dissociation of the stalled ribosomes. A central event is therefore the splitting of collided ribosomes by the ribosome quality control trigger complex, RQT, by an unknown mechanism. Here we show that RQT requires accessible mRNA and the presence of a neighboring ribosome. Cryogenic electron microscopy of RQT-ribosome complexes reveals that RQT engages the 40S subunit of the lead ribosome and can switch between two conformations. We propose that the Ski2-like helicase 1 (Slh1) subunit of RQT applies a pulling force on the mRNA, causing destabilizing conformational changes of the small ribosomal subunit, ultimately resulting in subunit dissociation. Our findings provide conceptual framework for a helicase-driven ribosomal splitting mechanism.


  • Organizational Affiliation

    Department of Biochemistry, Gene Center, Feodor-Lynen-Str. 25, University of Munich, 81377, Munich, Germany.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6D [auth A]224Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TIF6CDC95YPR016CLPZ15C
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AF [auth BA]105Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AG [auth BB]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AH [auth BC]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3I [auth BD]386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AJ [auth BE]361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5K [auth BF]296Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AL [auth BG]176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AM [auth BH]222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AN [auth BI]233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AO [auth BJ]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-BP [auth BL]169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AQ [auth BM]193Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AR [auth BN]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AS [auth BO]203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AT [auth BP]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AU [auth BQ]183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AV [auth BR]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AW [auth BS]160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AX [auth BT]172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AY [auth BU]159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AZ [auth BV]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AAA [auth BW]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-ABA [auth BX]69Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25CA [auth BY]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-ADA [auth BZ]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AEA [auth Ba]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28FA [auth Bb]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29GA [auth Bc]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30HA [auth Bd]97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AIA [auth Be]109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32JA [auth Bf]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AKA [auth Bg]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-ALA [auth Bh]112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AMA [auth Bi]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ANA [auth Bj]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AOA [auth Bk]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38PA [auth Bl]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39QA [auth Bm]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40-ARA [auth Bn]52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10SA [auth BK]220Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
25S ribosomal RNAA [auth 1]3,396Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth 3]121Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAC [auth 4]158Saccharomyces cerevisiae
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Entity ID: 5
MoleculeChains LengthOrganismImage
tRNAE [auth 2]76Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UNK
Query on UNK

Download Ideal Coordinates CCD File 
AB [auth 1]
BB [auth 1]
CB [auth 1]
DB [auth 1]
EB [auth 1]
AB [auth 1],
BB [auth 1],
CB [auth 1],
DB [auth 1],
EB [auth 1],
FB [auth 1],
GB [auth 1],
IB [auth BE],
JB [auth BE],
KB [auth BQ],
LB [auth BQ],
MB [auth BQ],
NB [auth BQ],
OB [auth Bm],
PB [auth Bm],
QB [auth Bm],
TA [auth 1],
UA [auth 1],
VA [auth 1],
WA [auth 1],
XA [auth 1],
YA [auth 1],
ZA [auth 1]
UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
HB [auth 2]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union885711
German Research Foundation (DFG)GermanyBE 1814/15-1
German Research Foundation (DFG)GermanyRTG1721

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references