6D90

Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES.

Pisareva, V.P.Pisarev, A.V.Fernandez, I.S.

(2018) Elife 7

  • DOI: 10.7554/eLife.34062
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its structural genes in the late stage of infection. Ribosome ...

    Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its structural genes in the late stage of infection. Ribosome hijacking is achieved by a sophisticated use of molecular mimicry to tRNA and mRNA, employed to manipulate intrinsically dynamic components of the ribosome. Binding and translocation through the ribosome is required for this IRES to initiate translation. We report two structures, solved by single particle electron cryo-microscopy (cryoEM), of a double translocated CrPV-IRES with aminoacyl-tRNA in the peptidyl site (P site) of the ribosome. CrPV-IRES adopts a previously unseen conformation, mimicking the acceptor stem of a canonical E site tRNA. The structures suggest a mechanism for the positioning of the first aminoacyl-tRNA shared with the distantly related Hepatitis C Virus IRES.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
uL3
B
403Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
uL4
C
392Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
uL18
D
297Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL5
Find proteins for G1SYJ6 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
eL6
E
291Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL6
Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
uL30
F
249Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL7
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
eL8
G
242Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354898
Find proteins for G1STW0 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
uL6
H
192Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354760
Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
uL11
J
178Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
eL13
L
211Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
eL14
M
198Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
Find proteins for U3KNW6 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
uL13
O
199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uL22
P
184Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL17-C18orf32
Find proteins for G1TVT6 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
rL18
Q
188Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TX70 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eL19
R
181Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL21
T
160Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eL22
U
128Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL22
Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
uL14
V
140Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL23
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
eL24
W
157Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
eL23
X
156Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100350855
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uL24
Y
145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
eL27
Z
136Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356974RPL27
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
eL29
b
226Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL29
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eL33
f
110Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35A
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eL34
g
126Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354714
Find proteins for G1U945 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
eL35
h
123Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eL36
i
105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
eL37
j
97Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
eL39
l
51Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100343258
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
eL40
m
52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
eL41
n
25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eL28
r
137Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100358162
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
uL1
K
217Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10A
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
uS2
BB
295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSALOC100340199
Find proteins for G1TWL4 (Oryctolagus cuniculus)
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
eS1
CC
264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3ALOC100342838LOC100348981
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
eS4
FF
263Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
uS7
GG
204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
eS6
HH
249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
eS7
II
194Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
eS8
JJ
208Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
uS4
KK
194Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
eS10
LL
149Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
Find proteins for G1TPV3 (Oryctolagus cuniculus)
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
uS17
MM
158Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
eS12
NN
132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
uS9
RR
172Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
eS17
SS
135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606RPS17
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
uS13
TT
152Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
eS19
UU
145Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
uS10
VV
119Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS20LOC100341365LOC100348955LOC100354063
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
eS21
WW
83Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
Find proteins for G1TM82 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
uS8
XX
130Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
uS12
YY
143Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
eS24
ZZ
134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS24
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
eS25
aa
125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
eS26
bb
115Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100346996
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
eS27
cc
84Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694LOC100345044LOC100348261RPS27
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
eS29
ee
56Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
eS30
ff
133Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
eS31
gg
156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
eRF1
jj
437Homo sapiensMutation(s): 0 
Gene Names: ETF1ERF1RF1SUP45L1
Find proteins for P62495 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P62495
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
uL2
A
257Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
eL15
N
204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
eL20
S
176Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL18A
Find proteins for G1TTY7 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
uL15
a
148Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27ALOC100350771
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eL30
c
115Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL30
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eL31
d
125Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
eL32
e
135Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL32
Find proteins for G1U437 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eL38
k
70Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352574
Find proteins for G1U001 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL42
o
106Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100342087
Find proteins for G1U344 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
eL43
p
92Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807LOC100349729RPL37A
Find proteins for G1SY53 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SY53
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
uL10
s
303Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
uL11
t
195Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL12
Find proteins for G1SMR7 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SMR7
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
uS5
DD
255Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SWM1 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SWM1
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
uS3
EE
281Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
Find proteins for G1TNM3 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TNM3
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
uS15
OO
151Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SP51 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SP51
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
uS11
PP
151Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337691
Find proteins for G1U472 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U472
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
uS19
QQ
145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U0Q2
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
eS28
dd
69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TIB4
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
RACK1
hh
317Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SJB4
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
uL16
I
214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
Go to UniProtKB:  B7NZQ2
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Entity ID: 45
MoleculeChainsLengthOrganism
28S rRNA53594Oryctolagus cuniculus

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Entity ID: 46
MoleculeChainsLengthOrganism
5S rRNA7119Oryctolagus cuniculus

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Entity ID: 47
MoleculeChainsLengthOrganism
5.8S rRNA8151Oryctolagus cuniculus

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Entity ID: 50
MoleculeChainsLengthOrganism
P-tRNA387Escherichia coli

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Entity ID: 85
MoleculeChainsLengthOrganism
CrPV-IRES4194Cricket paralysis virus

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Entity ID: 49
MoleculeChainsLengthOrganism
18S rRNA21697Oryctolagus cuniculus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM097014

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other