6T83

Structure of yeast disome (di-ribosome) stalled on poly(A) tract.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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 S7-A
Hb, i
190Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
Ib, j
200Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
Jb, k
197Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A
Kb, l
105Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
Lb, m
156Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
Mb, n
143Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
Nb, o
151Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-A
Ob, p
137Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
Qb, r
143Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-B
Rb, s
136Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P14127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
Ab, b
252Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
Sb, t
146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
Tb, u
144Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
Ub, v
121Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
Vb, w
87Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
Wb, x
130Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
Xb, y
145Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
Yb, z
135Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
0, Zb
108Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-A
1, ab
119Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
2, bb
82Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
Ba, c
255Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
4, db
56Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
5, eb
63Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
6, fb
152Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
7, gb
319Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-B
3, cb
67Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C0X0 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
Ay, Da
254Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
By, Ea
387Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
Cy, Fa
362Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
Pb, q
142Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
Dy, Ga
297Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
Ey, Ha
176Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
Fy, Ia
244Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
Gy, Ja
256Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
Hy, Ka
191Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
Iy, La
221Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-A
Jy, Ma
174Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
Ly, Na
199Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
My, Oa
138Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
Ny, Pa
204Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
Cb, d
254Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
Oy, Qa
199Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
A, Py
184Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
B, Qy
186Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
C, Ry
189Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
D, Sy
172Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
E, Ty
160Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
F, Uy
121Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
G, Vy
137Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
H, Wy
155Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
I, Xy
142Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
Db, e
240Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
J, Yy
127Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
K, Zy
136Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
L, ay
149Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
M, by
59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
N, cy
105Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
O, dy
113Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
P, ey
130Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
Q, fy
107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
R, gy
121Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
S, hb
120Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
Eb, f
261Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
T, ib
100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
U, jb
88Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
V, kb
78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
W, lb
51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
X, mb
128Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-A
Y, nb
25Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
Z, ob
106Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
aa, pb
92Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Rps5p
Fb, g
225Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS5
Find proteins for A0A1L4AA68 (Saccharomyces cerevisiae)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
ba
311Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
Gb, h
236Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsLengthOrganism
18S rRNA2b, a1800Saccharomyces cerevisiae

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Entity ID: 35
MoleculeChainsLengthOrganism
5S rRNA4b, Bb121Saccharomyces cerevisiae

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Entity ID: 36
MoleculeChainsLengthOrganism
5.8S rRNA3b, Ca158Saccharomyces cerevisiae

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Entity ID: 78
MoleculeChainsLengthOrganism
25S rRNA1b, Aa3396Saccharomyces cerevisiae

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Entity ID: 79
MoleculeChainsLengthOrganism
tRNA6b, 876Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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