5MC6

Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 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

The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex.

Schmidt, C., Kowalinski, E., Shanmuganathan, V., Defenouillere, Q., Braunger, K., Heuer, A., Pech, M., Namane, A., Berninghausen, O., Fromont-Racine, M., Jacquier, A., Conti, E., Becker, T., Beckmann, R.

(2016) Science 354: 1431-1433

  • DOI: 10.1126/science.aaf7520

  • PubMed Abstract: 

    • Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski complex directly associates with 80S ribosomes pres ...

    Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski complex directly associates with 80S ribosomes presenting a short mRNA 3' overhang. We determined the structure of an endogenous ribosome-Ski complex using cryo-electron microscopy (EM) with a local resolution of the Ski complex ranging from 4 angstroms (Å) in the core to about 10 Å for intrinsically flexible regions. Ribosome binding displaces the autoinhibitory domain of the Ski2 helicase, positioning it in an open conformation near the ribosomal mRNA entry tunnel. We observe that the mRNA 3' overhang is threaded directly from the small ribosomal subunit to the helicase channel of Ski2, primed for ongoing exosome-mediated 3'-5' degradation.

    Organizational Affiliation: 

    Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Rue du Docteur Roux 25-28, 75724 Paris, France.,Sorbonne Universités, UPMC Paris 6, Complexité du Vivant, 75252 Paris Cedex 05, France.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany. beckmann@genzentrum.lmu.de becker@genzentrum.lmu.de conti@biochem.mpg.de.,Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152 Martinsried, Munich, Germany. beckmann@genzentrum.lmu.de becker@genzentrum.lmu.de conti@biochem.mpg.de.,Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152 Martinsried, Munich, Germany.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
A
240Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS3 (SUF14)
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P05750
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
B
225Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS5 (RPS2)
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A
C
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS10A
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08745
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
D
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS12
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
E
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS15 (RPS21)
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q01855
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
F
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS16A (RP61R)
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-B
G
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS17B (RP51B)
Find proteins for P14127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
H
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS18A
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
I
144Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS19A (RP55A, RPS16AA)
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07280
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
J
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS20 (URP2)
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
K
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS25A (RPS31A)
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-B
L
67Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS28B (RPS33B)
Find proteins for P0C0X0 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
M
56Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS29A (RPS36A, YS29A)
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41057
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
N
152Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS31 (RPS37, UBI3)
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05759
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
O
319Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ASC1 (CPC2)
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
P
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS0A (NAB1, NAB1A, YST1)
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32905
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
Q
255Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS1A (PLC1, RPS10A)
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
R
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS2 (RPS4, SUP38, SUP44)
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
S
261Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS4A (RPS7B)
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
T
236Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
U
190Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS7A (RPS30)
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
V
200Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS8A (RPS14A)
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
W
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS9A (RPS13A, YS11A)
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13516
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
X
156Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
Y
151Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS13 (RPS13C)
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS13
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-A
Z
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS14A (CRY1, RPL59)
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06367
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
a
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS21A (RPS25, RPS25A, RPS26A)
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
b
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS22A (RPS24, RPS24A)
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W1
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
c
145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS23A (RPS28A)
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX29
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
d
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS24A (RPS24EA)
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX31
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-A
e
119Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS26A (RPS26)
Find proteins for P39938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39938
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
f
82Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS27A
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS27A
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
g
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS30A
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX33
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Antiviral helicase SKI2
h
1287Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SKI2
EC: 3.6.4.13
Find proteins for P35207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P35207
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Superkiller protein 3
i
1432Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SKI3
Find proteins for P17883 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17883
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Antiviral protein SKI8
j, k
397Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SKI8 (REC103)
Find proteins for Q02793 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02793
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
AA
256Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17076
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
AB
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL23A
Go to UniProtKB:  P0CX41
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
AC
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL36A (RPL39A)
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL36A
Go to UniProtKB:  P05745
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
AD
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
AE
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
AF
88Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL37A
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-A
AG
174Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL11A (RP39A, RPL16A)
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
AH
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
AI
78Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL38
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
AJ
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
AK
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05743
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
AL
51Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL39 (RPL46, SPB2)
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
AM
138Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
AN
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL27A (RPL27)
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
AO
128Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL40A (UBI1)
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
AP
106Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
AQ
204Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05748
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
AR
149Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P02406
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-A
AS
25Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL41A (RPL47A, YL41A)
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
AT
92Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL43A
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
AU
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26784
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
AV
59Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL29 (YL43)
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P05747
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
AW
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL2A (RPL5B)
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
AX
184Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05740
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
AY
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL30 (RPL32)
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
uL1
AZ
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
BA
387Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P14126
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
BB
186Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
BC
113Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL31A (RPL34, RPL34A)
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C2H8
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
BD
221Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL10 (GRC5, QSR1)
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL10
Go to UniProtKB:  P41805
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
BE
362Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL4A (RPL2, RPL2A)
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P10664
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
BF
189Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL19A (RPL23A, YL14A)
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX82
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
BG
130Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL32
Go to UniProtKB:  P38061
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
BH
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX23
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
BI
297Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL5
Go to UniProtKB:  P26321
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
BJ
160Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL21A (URP1)
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02753
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
BK
107Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL33A (RPL37A)
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05744
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
BL
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL22A
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05749
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
BM
176Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL6A (RPL17A, YL16A)
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02326
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
BN
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL34A
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P87262
Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
BO
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL7A
Go to UniProtKB:  P05737
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
BP
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL35A
Go to UniProtKB:  P0CX84
Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 5A-1
BT
157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HYP2 (TIF51A)
Find proteins for P23301 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23301
Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNA21800Saccharomyces cerevisiae S288C
Entity ID: 35
MoleculeChainsLengthOrganism
mRNAl34Saccharomyces cerevisiae S288C
Entity ID: 36
MoleculeChainsLengthOrganism
A-site tRNAm76Saccharomyces cerevisiae S288C
Entity ID: 37
MoleculeChainsLengthOrganism
P-site tRNAn77Saccharomyces cerevisiae S288C
Entity ID: 83
MoleculeChainsLengthOrganism
25S ribosomal RNABQ3396Saccharomyces cerevisiae S288C
Entity ID: 84
MoleculeChainsLengthOrganism
5S ribosomal RNABR121Saccharomyces cerevisiae S288C
Entity ID: 85
MoleculeChainsLengthOrganism
5.8S ribosomal RNABS158Saccharomyces cerevisiae S288C
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
AZ
L-PEPTIDE LINKINGC4 H9 N O2

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5CT
Query on 5CT
BT
peptide linkingC10 H23 N3 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Data collection, Derived calculations
  • Version 1.2: 2018-11-21
    Type: Advisory, Data collection, Derived calculations