6I7O

The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 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

Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways.

Ikeuchi, K., Tesina, P., Matsuo, Y., Sugiyama, T., Cheng, J., Saeki, Y., Tanaka, K., Becker, T., Beckmann, R., Inada, T.

(2019) EMBO J 38

  • DOI: 10.15252/embj.2018100276
  • Primary Citation of Related Structures:  
    6I7O

  • PubMed Abstract: 

    • Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome ...

    Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo-EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2-mediated cleavages upstream of the disome, governed by initial Not4-mediated monoubiquitination of eS7 and followed by Hel2-mediated K63-linked polyubiquitination. We propose that Hel2-mediated ribosome ubiquitination is required both for canonical NGD (NGD RQC + ) and RQC coupled to the disome and that RQC-uncoupled NGD outside the disome (NGD RQC - ) can occur in a Not4-dependent manner.

    Organizational Affiliation: 

    Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-A AW, XW252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3 BA, YA386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-A BE, YE361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5 BI, YI294Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-A BM, YM176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-A BO, YO223Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-A AA, XA231Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-A AD, XD190Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10 BD, YD221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-B AG, XG169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-A AJ, XJ194Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-A AM, XM137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-A AQ, XQ203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-A AU, XU197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-A P, Pb206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-A Q, Qb216Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2 R, Rb217Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3 A, Ab223Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-A S, Sb260Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5 B, Bb206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-A T, Tb218Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-A U, Ub185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-A V, Vb200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-A W, Wb185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-A C, Cb92Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-A X, Xb146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12 D, Db124Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13 Y, Yb150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-B Z, Zb128Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15 E, Eb119Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-A F, Fb141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-A G, Gb125Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-A H, Hb145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-A I, Ib143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20 J, Jb101Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-A a, ab87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-A b, bb129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-A c, cb144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-A d, db134Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-A K, Kb69Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-B e, eb97Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-A f, fb81Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-A L, Lb63Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-A M, Mb53Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-A g, gb60Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31 N, Nb73Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like protein O, Ob313Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-A AX, XX184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-A BB, YB185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-A BF, YF188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-A BH, YH172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-A BJ, YJ159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-A BL, YL98Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-A AB, XB134Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-A AE, XE135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25 AH, XH120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-A AK, XK124Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-A AN, XN135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28 AR, XR148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29 AV, XV58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein L30 AY, XY100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein L31-A BC, YC109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S ribosomal protein L32 BG, YG127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-A BK, YK106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L34-A BN, YN112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S ribosomal protein L35-A BP, YP119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L36-A AC, XC99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L37-A AF, XF82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L38 AI, XI77Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39 AL, XL50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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Ubiquitin-60S ribosomal protein L40 AO, XO52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L41-B AS, XS25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L42-A AP, XP105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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60S ribosomal protein L43-A AT, XT91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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60S acidic ribosomal protein P0 BU, YU312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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25S ribosomal RNABQ, YQ3396Saccharomyces cerevisiae
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Entity ID: 2
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5S ribosomal RNABR, YR121Saccharomyces cerevisiae
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Entity ID: 3
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5.8S ribosomal RNABS, YS157Saccharomyces cerevisiae
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Entity ID: 18
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18S ribosomal RNA2, 2b1800Saccharomyces cerevisiae
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Entity ID: 80
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P-site tRNAn76Saccharomyces cerevisiae
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Entity ID: 81
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E-site tRNAm75Saccharomyces cerevisiae
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Entity ID: 82
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A/P hybrid tRNAnb76Saccharomyces cerevisiae
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Entity ID: 83
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P/E hybrid tRNAmb77Saccharomyces cerevisiae
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Entity ID: 84
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mRNAl57Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanyBE1814/15-1
Japan Society for the Promotion of ScienceJapan26116003

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references