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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AD [auth AW],
ND [auth XW],
QG [auth zW]
254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3E [auth BA],
OD [auth YA],
RG [auth ZA]
387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AF [auth BE],
PD [auth YE],
SG [auth ZE]
362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5G [auth BI],
QD [auth YI],
TG [auth ZI]
297Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AH [auth BM],
RD [auth YM],
UG [auth ZM]
176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AI [auth BO],
SD [auth YO],
VG [auth ZO]
244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AJ [auth AA],
TD [auth XA],
WG [auth zA]
256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AK [auth AD],
UD [auth XD],
XG [auth zD]
190Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10L [auth BD],
VD [auth YD],
YG [auth ZD]
221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AM [auth AG],
WD [auth XG],
ZG [auth zG]
174Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AAH [auth zJ],
N [auth AJ],
XD [auth XJ]
199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-ABH [auth zM],
O [auth AM],
YD [auth XM]
138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-ACH [auth zQ],
P [auth AQ],
ZD [auth XQ]
204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AAE [auth XU],
DH [auth zU],
Q [auth AU]
199Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-ADC [auth Pb],
GF [auth Pc],
S [auth P]
252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AEC [auth Qb],
HF [auth Qc],
T [auth Q]
255Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2FC [auth Rb],
IF [auth Rc],
U [auth R]
254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3GC [auth Ab],
JF [auth Ac],
V [auth A]
240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AHC [auth Sb],
KF [auth Sc],
W [auth S]
261Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Rps5pIC [auth Bb],
LF [auth Bc],
X [auth B]
225Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AJC [auth Tb],
MF [auth Tc],
Y [auth T]
218Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AKC [auth Ub],
NF [auth Uc],
Z [auth U]
190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AAA [auth V],
LC [auth Vb],
OF [auth Vc]
200Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-ABA [auth W],
MC [auth Wb],
PF [auth Wc]
197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-ACA [auth C],
NC [auth Cb],
QF [auth Cc]
92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-ADA [auth X],
OC [auth Xb],
RF [auth Xc]
156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12EA [auth D],
PC [auth Db],
SF [auth Dc]
143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13FA [auth Y],
QC [auth Yb],
TF [auth Yc]
151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AGA [auth Z],
RC [auth Zb],
UF [auth Zc]
137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15HA [auth E],
SC [auth Eb],
VF [auth Ec]
142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AIA [auth F],
TC [auth Fb],
WF [auth Fc]
143Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-BJA [auth G],
UC [auth Gb],
XF [auth Gc]
136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AKA [auth H],
VC [auth Hb],
YF [auth Hc]
146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-ALA [auth I],
WC [auth Ib],
ZF [auth Ic]
144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20AG [auth Jc],
MA [auth J],
XC [auth Jb]
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-ABG [auth ac],
NA [auth a],
YC [auth ab]
87Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-ACG [auth bc],
OA [auth b],
ZC [auth bb]
130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AAD [auth cb],
DG [auth cc],
PA [auth c]
145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-ABD [auth db],
EG [auth dc],
QA [auth d]
135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-ACD [auth Kb],
FG [auth Kc],
RA [auth K]
108Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26-ADD [auth eb],
GG [auth ec],
SA [auth e]
119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AED [auth fb],
HG [auth fc],
TA [auth f]
82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-BFD [auth Lb],
IG [auth Lc],
UA [auth L]
67Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29-AGD [auth Mb],
JG [auth Mc],
VA [auth M]
56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AHD [auth gb],
KG [auth gc],
WA [auth g]
63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31ID [auth Nb],
LG [auth Nc],
XA [auth N]
152Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinJD [auth Ob],
MG [auth Oc],
YA [auth O]
319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-ABE [auth XX],
EH [auth zX],
ZA [auth AX]
184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AAB [auth BB],
CE [auth YB],
FH [auth ZB]
186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-ABB [auth BF],
DE [auth YF],
GH [auth ZF]
189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-ACB [auth BH],
EE [auth YH],
HH [auth ZH]
172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-ADB [auth BJ],
FE [auth YJ],
IH [auth ZJ]
160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AEB [auth BL],
GE [auth YL],
JH [auth ZL]
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AFB [auth AB],
HE [auth XB],
KH [auth zB]
137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AGB [auth AE],
IE [auth XE],
LH [auth zE]
135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25HB [auth AH],
JE [auth XH],
MH [auth zH]
142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AIB [auth AK],
KE [auth XK],
NH [auth zK]
127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AJB [auth AN],
LE [auth XN],
OH [auth zN]
136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28KB [auth AR],
ME [auth XR],
PH [auth zR]
149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29LB [auth AV],
NE [auth XV],
QH [auth zV]
59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30MB [auth AY],
OE [auth XY],
RH [auth zY]
105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-ANB [auth BC],
PE [auth YC],
SH [auth ZC]
113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32OB [auth BG],
QE [auth YG],
TH [auth ZG]
130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-APB [auth BK],
RE [auth YK],
UH [auth ZK]
107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AQB [auth BN],
SE [auth YN],
VH [auth ZN]
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-ARB [auth BP],
TE [auth YP],
WH [auth ZP]
120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ASB [auth AC],
UE [auth XC],
XH [auth zC]
100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ATB [auth AF],
VE [auth XF],
YH [auth zF]
88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38UB [auth AI],
WE [auth XI],
ZH [auth zI]
78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39AI [auth zL],
VB [auth AL],
XE [auth XL]
51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40BI [auth zO],
WB [auth AO],
YE [auth XO]
128Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-BCI [auth zS],
XB [auth AS],
ZE [auth XS]
25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AAF [auth XP],
DI [auth zP],
YB [auth AP]
106Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-ABF [auth XT],
EI [auth zT],
ZB [auth AT]
92Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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