6T4Q

Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts.

Tesina, P.Lessen, L.N.Buschauer, R.Cheng, J.Wu, C.C.Berninghausen, O.Buskirk, A.R.Becker, T.Beckmann, R.Green, R.

(2020) EMBO J 39: e103365-e103365

  • DOI: 10.15252/embj.2019103365
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro bioc ...

    Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall- and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes.


    Organizational Affiliation

    Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
SI
198Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
SJ
184Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A
SK
92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
SL
144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
SM
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
SN
150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-B
SO
127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
SQ
141Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-A
SR
125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
SS
145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
SB
232Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
ST
143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
SU
100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
SV
87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
SW
129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
SX
144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
SY
134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
SZ
82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-B
Sa
97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
Sb
81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
Sd
53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
SP
117Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
Se
60Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
Sf
73Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
Sg
312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-A
Sc
63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
LA
251Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
LB
386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
LC
361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
LD
294Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
SC
216Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-B
LE
175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
LF
222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
LG
233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
LH
191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
LI
218Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-B
LJ
169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
LL
193Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
LM
136Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
LN
203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
LO
197Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
SD
222Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
LP
183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
LQ
185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
LR
188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
LS
171Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
LT
159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
LU
100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
LV
136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
LW
126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
LX
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
LY
125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
SE
258Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
LZ
135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
La
148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
Lb
58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
Lc
96Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
Ld
109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
Le
127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
Lf
106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
Lg
112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
Lh
119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
Li
99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Rps5p
SF
206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS5
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
Lj
85Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
Lk
77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
Ll
50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
Lm
52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-A
Ln
25Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
Lo
103Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
Lp
91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
SG
228Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
nascent chain
8
6Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
SA
206Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
SH
184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
18S rRNAC21798Saccharomyces cerevisiae

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Entity ID: 34
MoleculeChainsLengthOrganism
5S rRNAC4121Saccharomyces cerevisiae

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Entity ID: 35
MoleculeChainsLengthOrganism
5.8S rRNAC3158Saccharomyces cerevisiae

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Entity ID: 77
MoleculeChainsLengthOrganism
25S rRNAC13184Saccharomyces cerevisiae

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Entity ID: 78
MoleculeChainsLengthOrganism
mRNA530Saccharomyces cerevisiae

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Entity ID: 79
MoleculeChainsLengthOrganism
ICG tRNA Arg (P/P)676Saccharomyces cerevisiae

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Entity ID: 80
MoleculeChainsLengthOrganism
tRNA (E/E)775Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
Lg, Lj, Lm, Lo, Lp, Sd, Sf
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
6, C1, C2, C3, C4, LA, LB, LF, LN, LP, LR, LV, La, Le, Lg, Lj, SF
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2020-02-12
    Changes: Database references