6SNT

Yeast 80S ribosome stalled on SDD1 mRNA.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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. Howeve ...

    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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AA252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AB255Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
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40S ribosomal protein S2C254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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40S ribosomal protein S3D240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
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40S ribosomal protein S4-AE261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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40S ribosomal protein S5F225Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
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40S ribosomal protein S6-AG236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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40S ribosomal protein S7-AH190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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40S ribosomal protein S8-AI200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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40S ribosomal protein S9-AJ197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
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40S ribosomal protein S10-AK105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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40S ribosomal protein S12M143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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40S ribosomal protein S13N151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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40S ribosomal protein S14-AO137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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40S ribosomal protein S16-AQ143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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40S ribosomal protein S17-BR136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AS146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-AT144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20U121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
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40S ribosomal protein S21-AV87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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40S ribosomal protein S22-AW130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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40S ribosomal protein S23-AX145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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40S ribosomal protein S24-AY135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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40S ribosomal protein S25-AZ105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
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40S ribosomal protein S26-Aa119Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-Ab82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
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40S ribosomal protein S29-Ad56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
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40S ribosomal protein S30-Ae63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
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Guanine nucleotide-binding protein subunit beta-like proteing319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
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40S ribosomal protein S28-Bc67Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
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60S ribosomal protein L2-Ah254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
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60S ribosomal protein L3i387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
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60S ribosomal protein L4-Aj362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5k297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
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60S ribosomal protein L6-Bl167Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-Am244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-An256Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-Ao191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10p221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
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60S ribosomal protein L11-Aq174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
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60S ribosomal protein L13-Ar199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-As138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-At204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-Au199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-Av184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-Aw186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-Ax189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-Ay172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-Az160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-Aau121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AAB137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-Aat155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25as142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
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60S ribosomal protein L26-Aar127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-Aaq136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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60S ribosomal protein L28ap149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein L29ao59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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60S ribosomal protein L30an105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein L31-Aam113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein L32al130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S ribosomal protein L33-Aak107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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60S ribosomal protein L34-Aaj121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L35-Aai120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S ribosomal protein L36-Aah100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L37-Aag88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L38af78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L39ae51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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Ubiquitin-60S ribosomal protein L40ad128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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L41-Aac25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L42-Aab106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L43-Aaa92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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Uncharacterized protein YEL057CNC233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
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40S ribosomal protein S11-AL156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
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Ubiquitin-40S ribosomal protein S31f152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
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40S ribosomal protein S15P142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNA21800Saccharomyces cerevisiae
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Entity ID: 35
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5S rRNA4121Saccharomyces cerevisiae
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Entity ID: 36
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5.8S rRNA3158Saccharomyces cerevisiae
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Entity ID: 78
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Saccharomyces cerevisiae S288C 25S ribosomal RNA (RDN25-1), rRNA13396Saccharomyces cerevisiae
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Entity ID: 79
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mRNA521Saccharomyces cerevisiae
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Entity ID: 81
MoleculeChainsLengthOrganismImage
tRNA676Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
aa, ab, ad, ag, aj, d, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
1, 2, 6, E, F, T
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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