6MTB

Rabbit 80S ribosome with P- and Z-site tRNAs (unrotated state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structures of translationally inactive mammalian ribosomes.

Brown, A.Baird, M.R.Yip, M.C.Murray, J.Shao, S.

(2018) Elife 7

  • DOI: 10.7554/eLife.40486
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze i ...

    The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.


    Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, United States.



Macromolecules

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
B
394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
D
293Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL5
Find proteins for G1SYJ6 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
E
291Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL6
Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7
F
247Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7a
G
319Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
I
214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11
J
178Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13
L
210Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14
M
138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
Find proteins for U3KNW6 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15
N
203Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17
P
153Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18
Q
187Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19
R
180Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18a
S
176Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21
T
159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22
U
99Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24
W
157Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23a
X
118Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26
Y
134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27
Z
135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356974RPL27
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27a
a
147Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27ALOC100350771
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
b
245Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
c
98Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL30
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31
d
107Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
e
128Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35a
f
109Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35A
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34
g
114Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35
h
122Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36
i
102Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37
j
86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
l
50Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100343258
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36a
o
103Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353469
Find proteins for G1T040 (Oryctolagus cuniculus)
Go to UniProtKB:  G1T040

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
r
124Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100358162
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10a
u
206Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10A
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
BB
213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3ALOC100342838LOC100348981
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
CC
221Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
FF
204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
GG
237Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
HH
194Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
II
206Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9
JJ
185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10
KK
96Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
Find proteins for G1TPV3 (Oryctolagus cuniculus)
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
LL
158Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
MM
117Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
NN
149Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
OO
136Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
PP
120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
QQ
142Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17
RR
132Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606RPS17
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
TT
141Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
UU
100Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
VV
83Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15a
WW
129Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
XX
141Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
YY
124Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25
ZZ
75Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26
aa
101Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
bb
83Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28
cc
62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29
dd
55Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
ee
55Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27a
ff
68Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
Receptor of activated protein C kinase 1
gg
313Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9
H
190Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354760
Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13a
O
199Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23
V
131Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL23
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
k
69Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L40
m
52Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41
n
25Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37a
p
91Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807LOC100349729RPL37A
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
AA
217Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
DD
228Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4, X isoform
EE
262Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
SS
144Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8
A
248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4
C
362Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChainsLengthOrganism
Z-site tRNA475Oryctolagus cuniculus

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Entity ID: 6
MoleculeChainsLengthOrganism
5.8S rRNA8151Oryctolagus cuniculus
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Entity ID: 1
MoleculeChainsLengthOrganism
mRNA17unidentified

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Entity ID: 2
MoleculeChainsLengthOrganism
P-site tRNA276Oryctolagus cuniculus

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Entity ID: 4
MoleculeChainsLengthOrganism
28S rRNA53597Oryctolagus cuniculus

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Entity ID: 5
MoleculeChainsLengthOrganism
5S rRNA7120Oryctolagus cuniculus

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Entity ID: 50
MoleculeChainsLengthOrganism
18S rRNA91698Oryctolagus cuniculus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
aa, dd, ff, g, j, m, o, p
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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5, 7, 8, 9, A, P, Q, V, a, aa
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
mL-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2019-05-15
    Changes: Atomic model, Data collection, Derived calculations, Polymer sequence