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
  • Structures With Same Primary Citation

  • 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: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
B
255Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
P
142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
C
254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
D
240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
E
261Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
F
225Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
G
236Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
H
190Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
I
200Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
J
197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A
K
105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
L
156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
M
143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
N
151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-A
O
137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
Q
143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-B
R
136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
S
146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
T
144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
U
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
V
87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
W
130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
X
145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
Y
135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-A
a
119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
b
82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
e
63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
f
152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
g
319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-B
c
67Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
j
362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
k
297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-B
l
167Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
m
244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
n
256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
o
191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
p
221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-A
q
174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
r
199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
s
138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
t
204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
u
199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
v
184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
w
186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
x
189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
y
172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
au
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
AB
137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
at
155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
as
142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
ar
127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
aq
136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
ap
149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
ao
59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
an
105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
am
113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
al
130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
ak
107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
aj
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
ai
120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
ah
100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
ag
88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
af
78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
ae
51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
ad
128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
ab
106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
aa
92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein YEL057C
NC
233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
A
252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
Z
105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
d
56Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41057
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
h
254Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX45
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
i
387Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P14126
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
z
160Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02753
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
L41-A
ac
25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsLengthOrganism
5S rRNA4121Saccharomyces cerevisiae

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Entity ID: 36
MoleculeChainsLengthOrganism
5.8S rRNA3158Saccharomyces cerevisiae

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Entity ID: 79
MoleculeChainsLengthOrganism
mRNA521Saccharomyces cerevisiae

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Entity ID: 1
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNA21800Saccharomyces cerevisiae

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Entity ID: 78
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae S288C 25S ribosomal RNA (RDN25-1), rRNA13396Saccharomyces cerevisiae

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Entity ID: 81
MoleculeChainsLengthOrganism
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