3JAG

Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAA stop codon


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 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

Structural basis for stop codon recognition in eukaryotes.

Brown, A.Shao, S.Murray, J.Hegde, R.S.Ramakrishnan, V.

(2015) Nature 524: 493-496

  • DOI: 10.1038/nature14896
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and ...

    Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5-3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination.


    Organizational Affiliation

    MRC-LMB, Francis Crick Avenue, Cambridge, CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
uL2
A
244Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL8
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Go to UniProtKB:  G1TT27
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
uL3
B
394Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
Find proteins for G1TL06 (Oryctolagus cuniculus)
Go to Gene View: RPL3
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
uL4
C
362Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
Find proteins for G1SVW5 (Oryctolagus cuniculus)
Go to Gene View: RPL4
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
uL18
D
292Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL5
Find proteins for G1SYJ6 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
eL6
E
248Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG04 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TG04
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
uL30
F
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
eL8
G
241Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1STW0 (Oryctolagus cuniculus)
Go to UniProtKB:  G1STW0
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
uL6
H
190Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TX33 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
uL16
I
213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
uL5
J
169Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL11
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
eL13
L
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
eL14
M
138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
Find proteins for U3KNW6 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
eL15
N
203Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL15 (LOC100358370)
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
uL13
O
199N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uL22
P
153N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
eL18
Q
187N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eL19
R
180N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
eL20
S
175N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL21
T
159Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eL22
U
99N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
uL14
V
131Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL23
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
eL24
W
63Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TLD5 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
uL23
X
119Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC108177184 (LOC108177974)
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uL24
Y
134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
eL27
Z
135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356974 (RPL27)
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
uL15
a
147Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL27A
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
eL29
b
75Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL29
Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eL30
c
94N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eL31
d
107Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL31
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
eL32
e
128Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eL33
f
109Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35A
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eL34
g
114Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100354714
Find proteins for G1U945 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
uL29
h
122Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL35
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eL36
i
102Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348796
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
eL37
j
86Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eL38
k
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
eL39
l
50Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC108178831
Find proteins for G1SYU7 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
eL40
m
52N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
eL41
n
23Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL42
o
104Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353469
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
eL43
p
91Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100351807
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eL28
r
125Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100358162
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
uL10
s
198Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U6N2 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
uL11
t
163Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL12
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
peptide
1
15N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
uS2
AA
208N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
eS1
BB
213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A (LOC100342838, LOC100348981)
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
uS5
CC
218Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TUT9 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TUT9
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
uS3
DD
227Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
eS4
EE
262Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
uS7
FF
191Oryctolagus 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 
Gene Names: LOC100339133 (RPS6)
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
eS7
HH
189Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS7
Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
eS8
II
206Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
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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
98Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
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Go to UniProtKB:  G1TPV3
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
uS17
LL
152Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100347468
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
eS12
MM
124Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
uS15
NN
150Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS13
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
uS11
OO
136Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS14
Find proteins for G1T1F0 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
uS19
PP
127Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC103349305
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
uS9
QQ
141Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
eS17
RR
129Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS17
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
uS13
SS
137Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
Find proteins for G1SZI5 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
eS19
TT
141Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
uS10
UU
104Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100341365
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
eS21
VV
83Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
Find proteins for G1TM82 (Oryctolagus cuniculus)
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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 
Gene Names: RPS23
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
eS24
YY
126Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS24
Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
eS25
ZZ
75Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS25
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
eS26
aa
98N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
eS27
bb
83Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694 (LOC100345044, LOC100348261, RPS27)
Find proteins for G1TZ76 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TZ76
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
eS28
cc
61Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
uS14
dd
53Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U7M4
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
eS30
ee
57Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
eS31
ff
69Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348379
Find proteins for G1SK22 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SK22
Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
RACK1
gg
313Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
eRF1
ii
416Homo sapiensMutation(s): 2 
Gene Names: ETF1 (ERF1, RF1, SUP45L1)
Find proteins for P62495 (Homo sapiens)
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Entity ID: 87
MoleculeChainsSequence LengthOrganismDetails
ABCE1
jj
594Oryctolagus cuniculusMutation(s): 0 
Gene Names: ABCE1
Find proteins for G1SG72 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChainsLengthOrganism
tRNA(Val)276Oryctolagus cuniculus
Entity ID: 47
MoleculeChainsLengthOrganism
tRNA(Lys)375Oryctolagus cuniculus
Entity ID: 48
MoleculeChainsLengthOrganism
28S ribosomal RNA53662Oryctolagus cuniculus
Entity ID: 49
MoleculeChainsLengthOrganism
5S ribosomal RNA7120Oryctolagus cuniculus
Entity ID: 50
MoleculeChainsLengthOrganism
5.8S ribosomal RNA8156Oryctolagus cuniculus
Entity ID: 51
MoleculeChainsLengthOrganism
18S ribosomal RNA91719Oryctolagus cuniculus
Entity ID: 85
MoleculeChainsLengthOrganism
mRNAhh12Oryctolagus cuniculus
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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jj
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 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
ADP
Query on ADP

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jj
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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5, 7, 8, 9, C, g, hh, I, P, Q, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection