6SV4

The cryo-EM structure of SDD1-stalled collided trisome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1.

Matsuo, Y.Tesina, P.Nakajima, S.Mizuno, M.Endo, A.Buschauer, R.Cheng, J.Shounai, O.Ikeuchi, K.Saeki, Y.Becker, T.Beckmann, R.Inada, T.

(2020) Nat Struct Mol Biol 27: 323-332

  • DOI: 10.1038/s41594-020-0393-9
  • Primary Citation of Related Structures:  
    6SNT, 6SV4

  • PubMed Abstract: 
  • Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells that is triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation followed by degradation of nascent peptides. However, e ...

    Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells that is triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation followed by degradation of nascent peptides. However, endogenous RQC-inducing sequences and the mechanism underlying the ubiquitin-dependent ribosome dissociation remain poorly understood. Here, we identified SDD1 messenger RNA from Saccharomyces cerevisiae as an endogenous RQC substrate and reveal the mechanism of its mRNA-dependent and nascent peptide-dependent translational stalling. In vitro translation of SDD1 mRNA enabled the reconstitution of Hel2-dependent polyubiquitination of collided disomes and, preferentially, trisomes. The distinct trisome architecture, visualized using cryo-EM, provides the structural basis for the more-efficient recognition by Hel2 compared with that of disomes. Subsequently, the Slh1 helicase subunit of the RQC trigger (RQT) complex preferentially dissociates the first stalled polyubiquitinated ribosome in an ATP-dependent manner. Together, these findings provide fundamental mechanistic insights into RQC and its physiological role in maintaining cellular protein homeostasis.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan. toshifumi.inada.a3@tohoku.ac.jp.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-A AWXWzW254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
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60S ribosomal protein L3 BAYAZA387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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60S ribosomal protein L4-A BEYEZE362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
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60S ribosomal protein L5 BIYIZI297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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60S ribosomal protein L6-A BMYMZM176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
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60S ribosomal protein L7-A BOYOZO244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-A AAXAzA256Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-A ADXDzD190Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10 BDYDZD221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-A AGXGzG174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
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60S ribosomal protein L13-A AJXJzJ199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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60S ribosomal protein L14-A AMXMzM138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-A AQXQzQ204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-A AUXUzU199Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-A PPbPc252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-A QQbQc255Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2 RRbRc254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3 AAbAc240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-A SSbSc261Saccharomyces cerevisiaeMutation(s): 0 
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Rps5p BBbBc225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-A TTbTc218Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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40S ribosomal protein S7-A UUbUc190Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-A VVbVc200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
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40S ribosomal protein S9-A WWbWc197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
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40S ribosomal protein S10-A CCbCc92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
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40S ribosomal protein S11-A XXbXc156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
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40S ribosomal protein S12 DDbDc143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13 YYbYc151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-A ZZbZc137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
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40S ribosomal protein S15 EEbEc142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-A FFbFc143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-B GGbGc136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-A HHbHc146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
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40S ribosomal protein S19-A IIbIc144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20 JJbJc121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
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40S ribosomal protein S21-A aabac87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
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40S ribosomal protein S22-A bbbbc130Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-A ccbcc145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-A ddbdc135Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-A KKbKc108Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-A eebec119Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-A ffbfc82Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-B LLbLc67Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-A MMbMc56Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-A ggbgc63Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31 NNbNc152Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like protein OObOc319Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-A AXXXzX184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-A BBYBZB186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-A BFYFZF189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-A BHYHZH172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-A BJYJZJ160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-A BLYLZL121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-A ABXBzB137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-A AEXEzE135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
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60S ribosomal protein L25 AHXHzH142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-A AKXKzK127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-A ANXNzN136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28 ARXRzR149Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29 AVXVzV59Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30 AYXYzY105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein L31-A BCYCZC113Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
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60S ribosomal protein L32 BGYGZG130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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60S ribosomal protein L33-A BKYKZK107Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
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60S ribosomal protein L34-A BNYNZN121Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
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60S ribosomal protein L35-A BPYPZP120Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
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60S ribosomal protein L36-A ACXCzC100Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
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60S ribosomal protein L37-A AFXFzF88Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
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60S ribosomal protein L38 AIXIzI78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein L39 ALXLzL51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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Ubiquitin-60S ribosomal protein L40 AOXOzO128Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
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60S ribosomal protein L41-B ASXSzS25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L42-A APXPzP106Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
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60S ribosomal protein L43-A ATXTzT92Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 79
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60S acidic ribosomal protein P0 BUYUZU312Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
25S rRNABQ, YQ, ZQ3396Saccharomyces cerevisiae
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Entity ID: 2
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5S rRNABR, YR, ZR121Saccharomyces cerevisiae
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Entity ID: 3
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5.8S rRNABS, YS, ZS157Saccharomyces cerevisiae
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Entity ID: 18
MoleculeChainsLengthOrganismImage
18S rRNA2, 2b, 2c1800Saccharomyces cerevisiae
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Entity ID: 80
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tRNA (P/P)n76Saccharomyces cerevisiae
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Entity ID: 81
MoleculeChainsLengthOrganismImage
tRNA (A/P)nb, nc76Saccharomyces cerevisiae
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Entity ID: 82
MoleculeChainsLengthOrganismImage
tRNA (P/E)mb, mc77Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyBE1814/15-1

Revision History 

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-04-01
    Changes: Database references
  • Version 1.2: 2020-04-22
    Changes: Database references