7ZRS

Structure of the RQT-bound 80S ribosome from S. cerevisiae (C2) - composite map

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AF [auth AA]206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AG [auth AB]255Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RPS2 isoform 1H [auth AC]216Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RPS3 isoform 1I [auth AD]222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AJ [auth AE]258Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pK [auth AF]206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AL [auth AG]228Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AM [auth AH]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AN [auth AI]200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AO [auth AJ]184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AP [auth AK]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AQ [auth AL]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12R [auth AM]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13S [auth AN]150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BT [auth AO]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RPS15 isoform 1U [auth AP]117Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AV [auth AQ]141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AW [auth AR]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AX [auth AS]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AY [auth AT]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RPS20 isoform 1Z [auth AU]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AAA [auth AV]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RPS22A isoform 1BA [auth AW]129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-ACA [auth AX]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-ADA [auth AY]134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25EA [auth AZ]82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RPS26B isoform 1FA [auth Aa]97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AGA [auth Ab]81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
RPS28A isoform 1HA [auth Ac]63Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
RPS29A isoform 1IA [auth Ad]53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AJA [auth Ae]56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
RPS31 isoform 1KA [auth Af]73Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinLA [auth Ag]312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AMA [auth BA]251Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3NA [auth BB]386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
RPL4A isoform 1OA [auth BC]361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
RPL5 isoform 1PA [auth BD]294Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-BQA [auth BE]176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-ARA [auth BF]222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-ASA [auth BG]233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-ATA [auth BH]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
RPL10 isoform 1UA [auth BI]218Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
RPL11B isoform 1VA [auth BJ]169Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AWA [auth BK]193Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AXA [auth BL]136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AYA [auth BM]203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AZA [auth BN]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AAB [auth BO]183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-ABB [auth BP]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-ACB [auth BQ]188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-ADB [auth BR]171Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AEB [auth BS]159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AFB [auth BT]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AGB [auth BU]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
RPL24A isoform 1HB [auth BV]126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25IB [auth BW]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AJB [auth BX]125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AKB [auth BY]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28LB [auth BZ]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29MB [auth Ba]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30NB [auth Bb]96Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AOB [auth Bc]109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
RPL32 isoform 1PB [auth Bd]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AQB [auth Be]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-ARB [auth Bf]112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-ASB [auth Bg]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ATB [auth Bh]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AUB [auth Bi]85Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
RPL38 isoform 1VB [auth Bj]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39WB [auth Bk]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40-AXB [auth Bl]52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
RPL41A isoform 1YB [auth Bm]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AZB [auth Bn]103Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AAC [auth Bo]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
RQC trigger complex helicase SLH1BC [auth CA]1,967Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLH1, RQT2, YGR271W, G9365
EC: 3.6.4.13
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
RQC trigger complex subunit CUE3CC [auth CB]297Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CUE3, RQT3, YGL110C, G3060
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
RQC trigger complex subunit RQT4DC [auth CC]530Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RQT4, YKR023W
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNAA [auth 2]1,798Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAB [auth 3]158Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth 4]121Saccharomyces cerevisiae
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Entity ID: 4
MoleculeChains LengthOrganismImage
25S ribosomal RNAD [auth 5]3,396Saccharomyces cerevisiae
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Entity ID: 5
MoleculeChains LengthOrganismImage
tRNAE [auth 6]75Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
IC [auth Ad]
JC [auth Af]
KC [auth Bf]
LC [auth Bi]
MC [auth Bl]
IC [auth Ad],
JC [auth Af],
KC [auth Bf],
LC [auth Bi],
MC [auth Bl],
NC [auth Bn],
OC [auth Bo],
PC [auth CC],
QC [auth CC]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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EC [auth 2],
FC [auth 2],
GC [auth AE],
HC [auth AF]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
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