6R6G

Structure of XBP1u-paused ribosome nascent chain complex with SRP.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and mutational analysis of the ribosome-arresting human XBP1u.

Shanmuganathan, V.Schiller, N.Magoulopoulou, A.Cheng, J.Braunger, K.Cymer, F.Berninghausen, O.Beatrix, B.Kohno, K.Heijne, G.V.Beckmann, R.

(2019) Elife 8

  • DOI: 10.7554/eLife.46267
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM structure of the stalled human XBP1u AP. It forms a unique ...

    XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM structure of the stalled human XBP1u AP. It forms a unique turn in the ribosomal exit tunnel proximal to the peptidyl transferase center where it causes a subtle distortion, thereby explaining the temporary translational arrest induced by XBP1u. During ribosomal pausing the hydrophobic region 2 (HR2) of XBP1u is recognized by SRP, but fails to efficiently gate the Sec61 translocon. An exhaustive mutagenesis scan of the XBP1u AP revealed that only 8 out of 20 mutagenized positions are optimal; in the remaining 12 positions, we identify 55 different mutations increase the level of translational arrest. Thus, the wildtype XBP1u AP induces only an intermediate level of translational arrest, allowing efficient targeting by SRP without activating the Sec61 channel.


    Organizational Affiliation

    Gene Center, Department of Biochemistry, Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
eS31
0
68Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
uS14
9
55Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uL2
A
248Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
AA
55Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
uL3
B
394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
BB
189Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uL4
C
362Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
CC
206Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S9 (Predicted)
DD
185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 18
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: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S11
EE
151Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
X-box-binding protein 1
1
24Homo sapiensMutation(s): 0 
Gene Names: XBP1TREB5XBP2
Find proteins for P17861 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P17861

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6
E
251Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL6
Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S28
FF
62Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
uL30
F
225Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL7
Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S20
GG
100Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
eL8
G
240Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354898
Find proteins for G1STW0 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
uL6
H
190Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354760
Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
HH
83Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L10 (Predicted)
I
213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
uS13
II
144Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
Find proteins for G1SZI5 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
JJ
83Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694LOC100345044LOC100348261RPS27
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11
J
170Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eS17
KK
132Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606RPS17
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13
L
210Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TPV0 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26
LL
101Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L14
M
138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
Find proteins for U3KNW6 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
MM
136Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15
N
203Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
NN
124Oryctolagus 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 L13a
O
199Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS25
OO
75Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
uL22
P
153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL17-C18orf32
Find proteins for G1TVT6 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eS19
PP
141Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
eL18
Q
187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS15
QQ
149Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
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: 46
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
RR
117Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
eL20
S
176Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
eS10
SS
96Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
Find proteins for G1TPV3 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
eL21
T
159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15a
TT
129Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S16
UU
142Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 52
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: 53
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S23
VV
141Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
eL14
V
131Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL23
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24
W
121Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL24
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
uS19
WW
120Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
uL23
X
118Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100350855
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L26
Y
134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Entity ID: 59
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: 60
MoleculeChainsSequence LengthOrganismDetails
uL15
a
147Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27ALOC100350771
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
eL29
b
116Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL29
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
eL30
c
98Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL30
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
eL31
d
107Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
eL32
e
128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
eL33
f
109Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35A
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
eL34
g
114Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354714
Find proteins for G1U945 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
uL29
h
122Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36
i
102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37
j
86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RACK1
6
313Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 70
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: 71
MoleculeChainsSequence LengthOrganismDetails
eL39
l
50Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100343258
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 72
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: 73
MoleculeChainsSequence LengthOrganismDetails
60s ribosomal protein l41
n
25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
eL42
o
104Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353469
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eL43
p
91Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807LOC100349729RPL37A
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
uS2
q
217Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
eL28
r
124Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100358162
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
s
196Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
uL11
t
153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL12
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
u
213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3ALOC100342838LOC100348981
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
uS5
v
221Oryctolagus cuniculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S3
w
228Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4
x
262Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
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Go to UniProtKB:  G1TK17

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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S5
y
191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for G1TFM5 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TFM5

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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
z
237Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM55 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TM55

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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 54 kDa protein
AB
431Canis lupus familiarisMutation(s): 0 
Gene Names: SRP54
Find proteins for P61010 (Canis lupus familiaris)
Go to UniProtKB:  P61010

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Entity ID: 88
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP19
AC
105Canis lupus familiarisMutation(s): 0 
Gene Names: SRP19
Find proteins for J9PAS6 (Canis lupus familiaris)
Go to UniProtKB:  J9PAS6

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Entity ID: 89
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle subunit SRP68
AI
195Canis lupus familiarisMutation(s): 0 
Gene Names: SRP68
Find proteins for Q00004 (Canis lupus familiaris)
Go to UniProtKB:  Q00004

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Entity ID: 90
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 9 kDa protein
AD
74Canis lupus familiarisMutation(s): 0 
Gene Names: SRP9
Find proteins for F1Q0Z5 (Canis lupus familiaris)
Go to UniProtKB:  F1Q0Z5

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Entity ID: 91
MoleculeChainsSequence LengthOrganismDetails
Signal recognition particle 14 kDa protein
AE
94Canis lupus familiarisMutation(s): 0 
Gene Names: SRP14
Find proteins for P16255 (Canis lupus familiaris)
Go to UniProtKB:  P16255
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Entity ID: 92
MoleculeChainsSequence LengthOrganismDetails
Signal sequence (HR2)
AG
12Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 3
MoleculeChainsLengthOrganism
P-tRNA275Saccharomyces cerevisiae

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Entity ID: 31
MoleculeChainsLengthOrganism
18S ribosomal RNAK1698Oryctolagus cuniculus

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Entity ID: 4
MoleculeChainsLengthOrganism
E-tRNA375Saccharomyces cerevisiae
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Entity ID: 5
MoleculeChainsLengthOrganism
mRNA46Homo sapiens

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Entity ID: 6
MoleculeChainsLengthOrganism
28S ribosomal RNA53544Oryctolagus cuniculus

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Entity ID: 8
MoleculeChainsLengthOrganism
5S ribosomal RNA7120Oryctolagus cuniculus

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Entity ID: 87
MoleculeChainsLengthOrganism
7S RNAAF206Canis lupus familiaris

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Entity ID: 9
MoleculeChainsLengthOrganism
5.8S ribosomal RNA8151Oryctolagus cuniculus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download CCD File 
5, 7, 8, A, B, I, K, P, V, a, j
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK1721

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations