6MTD

Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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: 4
MoleculeChainsSequence LengthOrganismDetails
uL2
A
248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
uL3
B
394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
uL4
C
362Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
uL18
D
293Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL5
Find proteins for G1SYJ6 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
eL6
E
291Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL6
Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
uL30
F
225Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL7
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
eL8
G
319Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uL6
H
190Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354760
Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
uL16
I
214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
uL5
J
170Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
eL13
L
210Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
eL14
M
138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
Find proteins for U3KNW6 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
eL15
N
203Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
uL13
O
199Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
uL22
P
153Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL18
Q
187Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eL19
R
180Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q3T0W9 (Bos taurus)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
eL20
S
176Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A287APR1 (Sus scrofa)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
eL21
T
159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
eL22
U
99Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uL14
V
131Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL23
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
eL24
W
157Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
uL23
X
118Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q24JY1 (Bos taurus)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
uL24
Y
134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eL27
Z
135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356974RPL27
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
uL15
a
147Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27ALOC100350771
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
eL29
b
245Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eL30
c
98Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL30
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eL31
d
107Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
eL32
e
128Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL32
Find proteins for G1U437 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eL33
f
109Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35A
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
eL34
g
114Oryctolagus cuniculusMutation(s): 0 
Find proteins for P49207 (Homo sapiens)
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PHAROS  P49207

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
uL29
h
122Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
eL36
i
102Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
eL37
j
86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
eL38
k
69Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q32PB9 (Bos taurus)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL39
l
50Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100343258
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
eL40
m
52Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eL41
n
25Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
eL42
o
103Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353469
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
eL43
p
91Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807LOC100349729RPL37A
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
el28
r
124Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100358162
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
uL10
s
196Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q29214 (Sus scrofa)
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
eL11
t
153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL12
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
uL1
u
206Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10A
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
eEF2
v
839Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
SERBP1
w
26Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
uS2
AA
217Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
eS1
BB
213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3ALOC100342838LOC100348981
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
uS5
CC
221Oryctolagus cuniculusMutation(s): 0 
Find proteins for O18789 (Bos taurus)
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
uS3
DD
228Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
Find proteins for E2RH47 (Canis lupus familiaris)
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
eS4
EE
262Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q76N24 (Chlorocebus aethiops)
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
uS7
FF
204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
eS6
GG
237Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
eS7
HH
194Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
eS8
II
206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
uS4
JJ
185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
eS10
KK
96Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
Find proteins for G1TPV3 (Oryctolagus cuniculus)
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
uS17
LL
158Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
eS12
MM
117Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
uS15
NN
149Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
uS11
OO
136Oryctolagus cuniculusMutation(s): 0 
Find proteins for P13471 (Rattus norvegicus)
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
uS19
PP
120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
uS9
QQ
142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
eS17
RR
132Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606RPS17
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
uS13
SS
144Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
eS19
TT
141Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
uS10
UU
100Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q3ZBH8 (Bos taurus)
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
eS21
VV
83Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q32PB8 (Bos taurus)
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
uS8
WW
129Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
uS12
XX
141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
eS24
YY
124Oryctolagus cuniculusMutation(s): 0 
Find proteins for P62847 (Homo sapiens)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
eS25
ZZ
75Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
eS26
aa
101Oryctolagus cuniculusMutation(s): 0 
Find proteins for Q56JV1 (Bos taurus)
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
eS27
bb
83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
eS28
cc
62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
uS14
dd
55Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
eS30
ee
55Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
eS31
ff
68Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
RACK1
gg
313Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SJB4

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Entity ID: 1
MoleculeChainsLengthOrganism
28S rRNA53597Oryctolagus cuniculus

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Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNA7120Oryctolagus cuniculus

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Entity ID: 3
MoleculeChainsLengthOrganism
5.8S rRNA8151Oryctolagus cuniculus

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Entity ID: 51
MoleculeChainsLengthOrganism
18S rRNA91698Oryctolagus cuniculus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

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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, SS, TT, V, a, aa, dd, g, v
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
C
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
DDE
Query on DDE
C, v
L-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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 2.0: 2019-05-15
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Polymer sequence