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. However, endogenous RQC-inducing sequences and the mechanism underlying the ubiquitin-dependent ribosome dissociation remain poorly understood ...

    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.



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MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AB [auth A]252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AC [auth B]255Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15D [auth P]142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2E [auth C]254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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40S ribosomal protein S3F [auth D]240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-AG [auth E]261Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5H [auth F]225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AI [auth G]236Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AJ [auth H]190Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-AK [auth I]200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-AL [auth J]197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AM [auth K]105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AN [auth L]156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12O [auth M]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13P [auth N]151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-AQ [auth O]137Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AR [auth Q]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-BS [auth R]136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AT [auth S]146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-AU [auth T]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20V [auth U]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-AW [auth V]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-AX [auth W]130Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-AY [auth X]145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-AZ [auth Y]135Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-AAA [auth Z]105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-ABA [auth a]119Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-ACA [auth b]82Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-ADA [auth d]56Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-AEA [auth e]63Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31FA [auth f]152Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like proteinGA [auth g]319Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-BHA [auth c]67Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AKA [auth h]254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3LA [auth i]387Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AMA [auth j]362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5NA [auth k]297Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-BOA [auth l]167Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-APA [auth m]244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-AQA [auth n]256Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-ARA [auth o]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10SA [auth p]221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-ATA [auth q]174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AUA [auth r]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AVA [auth s]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
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60S ribosomal protein L15-AWA [auth t]204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AXA [auth u]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AYA [auth v]184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-AZA [auth w]186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AAB [auth x]189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
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60S ribosomal protein L20-ABB [auth y]172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
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60S ribosomal protein L21-ACB [auth z]160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
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60S ribosomal protein L22-ADB [auth au]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AEB [auth AB]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AFB [auth at]155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25GB [auth as]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
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60S ribosomal protein L26-AHB [auth ar]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-AIB [auth aq]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28JB [auth ap]149Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29KB [auth ao]59Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30LB [auth an]105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-AMB [auth am]113Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32NB [auth al]130Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-AOB [auth ak]107Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-APB [auth aj]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L35-AQB [auth ai]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S ribosomal protein L36-ARB [auth ah]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L37-ASB [auth ag]88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L38TB [auth af]78Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39UB [auth ae]51Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40VB [auth ad]128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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L41-AWB [auth ac]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein L42-AXB [auth ab]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L43-AYB [auth aa]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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Uncharacterized protein YEL057CBC [auth NC]233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNAA [auth 2]1,800Saccharomyces cerevisiae
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Entity ID: 35
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5S rRNAIA [auth 4]121Saccharomyces cerevisiae
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Entity ID: 36
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5.8S rRNAJA [auth 3]158Saccharomyces cerevisiae
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Entity ID: 78
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Saccharomyces cerevisiae S288C 25S ribosomal RNA (RDN25-1), rRNAZB [auth 1]3,396Saccharomyces cerevisiae
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Entity ID: 79
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mRNAAC [auth 5]21Saccharomyces cerevisiae
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Entity ID: 81
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tRNACC [auth 6]76Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
KF [auth d],
LF [auth f],
MF [auth aj],
NF [auth ag],
OF [auth ad],
KF [auth d],
LF [auth f],
MF [auth aj],
NF [auth ag],
OF [auth ad],
PF [auth ab],
QF [auth aa]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AD [auth 2],
AE [auth 2],
AF [auth 2],
BD [auth 2],
BE [auth 2],
AD [auth 2],
AE [auth 2],
AF [auth 2],
BD [auth 2],
BE [auth 2],
BF [auth 2],
CD [auth 2],
CE [auth 2],
CF [auth 2],
DC [auth 2],
DD [auth 2],
DE [auth 2],
DF [auth 2],
EC [auth 2],
ED [auth 2],
EE [auth 2],
EF [auth 2],
FC [auth 2],
FD [auth 2],
FE [auth 2],
FF [auth 2],
GC [auth 2],
GD [auth 2],
GE [auth 2],
GF [auth 2],
HC [auth 2],
HD [auth 2],
HE [auth 2],
HF [auth E],
IC [auth 2],
ID [auth 2],
IE [auth 2],
IF [auth F],
JC [auth 2],
JD [auth 2],
JE [auth 2],
JF [auth T],
KC [auth 2],
KD [auth 2],
KE [auth 2],
LC [auth 2],
LD [auth 2],
LE [auth 2],
MC [auth 2],
MD [auth 2],
ME [auth 2],
NC [auth 2],
ND [auth 2],
NE [auth 2],
OC [auth 2],
OD [auth 2],
OE [auth 2],
PC [auth 2],
PD [auth 2],
PE [auth 2],
QC [auth 2],
QD [auth 2],
QE [auth 2],
RC [auth 2],
RD [auth 2],
RE [auth 2],
RF [auth 1],
SC [auth 2],
SD [auth 2],
SE [auth 2],
SF [auth 6],
TC [auth 2],
TD [auth 2],
TE [auth 2],
UC [auth 2],
UD [auth 2],
UE [auth 2],
VC [auth 2],
VD [auth 2],
VE [auth 2],
WC [auth 2],
WD [auth 2],
WE [auth 2],
XC [auth 2],
XD [auth 2],
XE [auth 2],
YC [auth 2],
YD [auth 2],
YE [auth 2],
ZC [auth 2],
ZD [auth 2],
ZE [auth 2]
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

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyBE1814/15-1

Revision History  (Full details and data files)

  • 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