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 1.2 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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AD [auth AW],
MD [auth XW]
252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3E [auth BA],
ND [auth YA]
386Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AF [auth BE],
OD [auth YE]
361Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5G [auth BI],
PD [auth YI]
294Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AH [auth BM],
QD [auth YM]
176Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AI [auth BO],
RD [auth YO]
223Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AJ [auth AA],
SD [auth XA]
231Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AK [auth AD],
TD [auth XD]
190Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10L [auth BD],
UD [auth YD]
221Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-BM [auth AG],
VD [auth XG]
169Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AN [auth AJ],
WD [auth XJ]
194Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AO [auth AM],
XD [auth XM]
137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AP [auth AQ],
YD [auth XQ]
203Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AQ [auth AU],
ZD [auth XU]
197Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-ACC [auth Pb],
S [auth P]
206Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-ADC [auth Qb],
T [auth Q]
216Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2EC [auth Rb],
U [auth R]
217Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3FC [auth Ab],
V [auth A]
223Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AGC [auth Sb],
W [auth S]
260Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5HC [auth Bb],
X [auth B]
206Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AIC [auth Tb],
Y [auth T]
218Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AJC [auth Ub],
Z [auth U]
185Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AAA [auth V],
KC [auth Vb]
200Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-ABA [auth W],
LC [auth Wb]
185Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-ACA [auth C],
MC [auth Cb]
92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-ADA [auth X],
NC [auth Xb]
146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12EA [auth D],
OC [auth Db]
124Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13FA [auth Y],
PC [auth Yb]
150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BGA [auth Z],
QC [auth Zb]
128Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P39516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15HA [auth E],
RC [auth Eb]
119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AIA [auth F],
SC [auth Fb]
141Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AJA [auth G],
TC [auth Gb]
125Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AKA [auth H],
UC [auth Hb]
145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-ALA [auth I],
VC [auth Ib]
143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20MA [auth J],
WC [auth Jb]
101Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-ANA [auth a],
XC [auth ab]
87Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AOA [auth b],
YC [auth bb]
129Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-APA [auth c],
ZC [auth cb]
144Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AAD [auth db],
QA [auth d]
134Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-ABD [auth Kb],
RA [auth K]
69Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26-BCD [auth eb],
SA [auth e]
97Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-ADD [auth fb],
TA [auth f]
81Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AED [auth Lb],
UA [auth L]
63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29-AFD [auth Mb],
VA [auth M]
53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AGD [auth gb],
WA [auth g]
60Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31HD [auth Nb],
XA [auth N]
73Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinID [auth Ob],
YA [auth O]
313Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AAE [auth XX],
ZA [auth AX]
184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AAB [auth BB],
BE [auth YB]
185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-ABB [auth BF],
CE [auth YF]
188Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-ACB [auth BH],
DE [auth YH]
172Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-ADB [auth BJ],
EE [auth YJ]
159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AEB [auth BL],
FE [auth YL]
98Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AFB [auth AB],
GE [auth XB]
134Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AGB [auth AE],
HE [auth XE]
135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25HB [auth AH],
IE [auth XH]
120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AIB [auth AK],
JE [auth XK]
124Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AJB [auth AN],
KE [auth XN]
135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28KB [auth AR],
LE [auth XR]
148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29LB [auth AV],
ME [auth XV]
58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30MB [auth AY],
NE [auth XY]
100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-ANB [auth BC],
OE [auth YC]
109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32OB [auth BG],
PE [auth YG]
127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-APB [auth BK],
QE [auth YK]
106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AQB [auth BN],
RE [auth YN]
112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-ARB [auth BP],
SE [auth YP]
119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ASB [auth AC],
TE [auth XC]
99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ATB [auth AF],
UE [auth XF]
82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38UB [auth AI],
VE [auth XI]
77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39VB [auth AL],
WE [auth XL]
50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40WB [auth AO],
XE [auth XO]
52Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-BXB [auth AS],
YE [auth XS]
25Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AYB [auth AP],
ZE [auth XP]
105Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AAF [auth XT],
ZB [auth AT]
91Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0AC [auth BU],
BF [auth YU]
312Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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