6GQB

Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance.

Pellegrino, S.Demeshkina, N.Mancera-Martinez, E.Melnikov, S.Simonetti, A.Myasnikov, A.Yusupov, M.Yusupova, G.Hashem, Y.

(2018) J. Mol. Biol. 430: 2677-2687

  • DOI: 10.1016/j.jmb.2018.06.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), ...

    One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes.


    Organizational Affiliation

    ARNA, U1212 Université de Bordeaux, Institut Européen de Chimie et de Biologie (IECB) Inserm, Pessac 33600, France. Electronic address: yaser.hashem@u-bordeaux.fr.,Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France; Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia. Electronic address: marat@igbmc.fr.,Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France. Electronic address: gula@igbmc.fr.,Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg 67000, France.,Architecture and Reactivity of RNA, University of Strasbourg, Institute of Molecular and Cellular Biology of the CNRS UPR9002, Strasbourg 67084, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
P0
189Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPP0 (L10E, RPA0, RPL10E, RPLA0)
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05317
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12-A
P2
94Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL12A (RPL15B)
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX53
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
A
252Saccharomyces 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: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
B
386Saccharomyces 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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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
C
361Saccharomyces 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: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
D
296Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P26321
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
E
175Saccharomyces 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: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
F
222Saccharomyces 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: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
G
233Saccharomyces 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: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
H
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05738
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
I
220Saccharomyces 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: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-B
J
169Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL11B (RP39B, RPL16B)
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E757
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
L
193Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL13A
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
M
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36105
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
N
203Saccharomyces 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: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
O
197Saccharomyces 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: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
P
183Saccharomyces 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: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
Q
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL18A
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
R
188Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL19A (RPL23A, YL14A)
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
S
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
T
159Saccharomyces 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: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
U
100Saccharomyces 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: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
V
136Saccharomyces 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: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
W
64Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04449
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
X
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04456
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
Y
126Saccharomyces 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: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
Z
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL27A (RPL27)
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL27A
Go to UniProtKB:  P0C2H6
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
a
148Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL28
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
b
58Saccharomyces 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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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
c
97Saccharomyces 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: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
d
109Saccharomyces 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: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
e
127Saccharomyces 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: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
f
106Saccharomyces 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: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
g
112Saccharomyces 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: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
h
119Saccharomyces 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: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
i
99Saccharomyces 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: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
j
87Saccharomyces 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
Go to UniProtKB:  P49166
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
k
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL38
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL38
Go to UniProtKB:  P49167
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
l
50Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL39 (RPL46, SPB2)
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL39
Go to UniProtKB:  P04650
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
m
52Saccharomyces 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: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-B
n
25Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL41A (RPL47A, YL41A)
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX86
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
o
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX27
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
p
91Saccharomyces 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: 48
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
q
206Saccharomyces 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: 49
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
r
214Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS1A (PLC1, RPS10A)
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33442
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
s
217Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS2 (RPS4, SUP38, SUP44)
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS2
Go to UniProtKB:  P25443
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
t
223Saccharomyces 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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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
u
260Saccharomyces 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: 53
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
v
206Saccharomyces 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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Go to UniProtKB:  P26783
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
w
223Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX37
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
x
184Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS7A (RPS30)
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26786
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
y
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS8A (RPS14A)
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX39
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
z
185Saccharomyces 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: 58
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A
AA
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: 59
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
AB
153Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX47
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
AC
124Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS12
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS12
Go to UniProtKB:  P48589
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
AD
150Saccharomyces 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
Go to UniProtKB:  P05756
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-B
AE
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS14B (CRY2)
Find proteins for P39516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39516
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
AF
124Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS15 (RPS21)
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS15
Go to UniProtKB:  Q01855
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
AG
141Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS16A (RP61R)
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX51
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-B
AH
125Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS17B (RP51B)
Find proteins for P14127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P14127
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
AI
145Saccharomyces 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: 67
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
AJ
143Saccharomyces 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: 68
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
AK
107Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS20 (URP2)
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS20
Go to UniProtKB:  P38701
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
AL
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))
Go to UniProtKB:  P0C0V8
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
AM
129Saccharomyces 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: 71
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
AN
144Saccharomyces 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: 72
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
AO
134Saccharomyces 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: 73
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
AP
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS25A (RPS31A)
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E792
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-B
AQ
97Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS26B
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39939
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
AR
81Saccharomyces 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
Go to UniProtKB:  P35997
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-A
AS
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPS28A (RPS33, RPS33A)
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7X9
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
AT
53Saccharomyces 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: 78
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
AU
60Saccharomyces 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: 79
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
AV
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ASC1 (CPC2)
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38011
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
AW
37Saccharomyces 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: 83
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1-A
BA
204Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL1A (SSM1, SSM1A)
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX43
Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
Elongation factor 2
AZ
840Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EFT1, EFT2
Find proteins for P32324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32324
Entity ID: 1
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA13396Saccharomyces cerevisiae S288C
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA3121Saccharomyces cerevisiae S288C
Entity ID: 3
MoleculeChainsLengthOrganism
5.8S ribosomal RNA4158Saccharomyces cerevisiae S288C
Entity ID: 47
MoleculeChainsLengthOrganism
18S ribosomal RNA21797Saccharomyces cerevisiae S288C
Entity ID: 81
MoleculeChainsLengthOrganism
Transfer RNA - PheAX76Saccharomyces cerevisiae S288C
Entity ID: 82
MoleculeChainsLengthOrganism
Messenger RNAAY7Saccharomyces cerevisiae S288C
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
AZ
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
AQ, AR, AT, AW, j, m, o, p
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO1
Query on SO1

Download SDF File 
Download CCD File 
AZ
[1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID
SORDARIN
C27 H42 O8
DIBGPTPYRVEPSP-OHFCZZTFSA-N
 Ligand Interaction
ALF
Query on ALF

Download SDF File 
Download CCD File 
AZ
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DDE
Query on DDE
AZ
L-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FranceANR-15-CE11-0021-01
FranceFRM-DBF20160635745
ERC-294312
FranceANR-14-ACHN-0024

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-18
    Type: Data collection, Database references
  • Version 1.2: 2018-08-08
    Type: Data collection, Database references
  • Version 1.3: 2018-11-28
    Type: Data collection, Database references