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
  • Structures With Same Primary Citation

  • 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

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292Oryctolagus cuniculusMutation(s): 0 
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eL6
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248Oryctolagus cuniculusMutation(s): 0 
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225Oryctolagus cuniculusMutation(s): 0 
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203Oryctolagus cuniculusMutation(s): 0 
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eL21
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U
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V
131Oryctolagus cuniculusMutation(s): 0 
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eL24
W
63Oryctolagus cuniculusMutation(s): 0 
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119Oryctolagus cuniculusMutation(s): 0 
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Y
134Oryctolagus cuniculusMutation(s): 0 
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135Oryctolagus cuniculusMutation(s): 0 
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147Oryctolagus cuniculusMutation(s): 0 
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94Oryctolagus cuniculusMutation(s): 0 
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107Oryctolagus cuniculusMutation(s): 0 
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128Oryctolagus cuniculusMutation(s): 0 
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eL33
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109Oryctolagus cuniculusMutation(s): 0 
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114Oryctolagus cuniculusMutation(s): 0 
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122Oryctolagus cuniculusMutation(s): 0 
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eL36
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102Oryctolagus cuniculusMutation(s): 0 
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eL37
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86Oryctolagus cuniculusMutation(s): 0 
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eL38
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69Oryctolagus cuniculusMutation(s): 0 
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eL39
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50Oryctolagus cuniculusMutation(s): 0 
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eL40
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eL41
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23Oryctolagus cuniculusMutation(s): 0 
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104Oryctolagus cuniculusMutation(s): 0 
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eL43
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125Oryctolagus cuniculusMutation(s): 0 
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198Oryctolagus cuniculusMutation(s): 0 
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uS2
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eS1
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CC
218Oryctolagus cuniculusMutation(s): 0 
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227Oryctolagus cuniculusMutation(s): 0 
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eS4
EE
262Oryctolagus cuniculusMutation(s): 0 
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uS7
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191Oryctolagus cuniculusMutation(s): 0 
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eS6
GG
237Oryctolagus cuniculusMutation(s): 0 
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HH
189Oryctolagus cuniculusMutation(s): 0 
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206Oryctolagus cuniculusMutation(s): 0 
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uS4
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185Oryctolagus cuniculusMutation(s): 0 
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eS10
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98Oryctolagus cuniculusMutation(s): 0 
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uS17
LL
152Oryctolagus cuniculusMutation(s): 0 
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eS12
MM
124Oryctolagus cuniculusMutation(s): 0 
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uS15
NN
150Oryctolagus cuniculusMutation(s): 0 
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uS11
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136Oryctolagus cuniculusMutation(s): 0 
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uS19
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uS9
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141Oryctolagus cuniculusMutation(s): 0 
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eS17
RR
129Oryctolagus cuniculusMutation(s): 0 
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uS13
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137Oryctolagus cuniculusMutation(s): 0 
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eS19
TT
141Oryctolagus cuniculusMutation(s): 0 
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uS10
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MoleculeChainsSequence LengthOrganismDetails
eS21
VV
83Oryctolagus cuniculusMutation(s): 0 
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uS8
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129Oryctolagus cuniculusMutation(s): 0 
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uS12
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141Oryctolagus cuniculusMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
eS24
YY
126Oryctolagus cuniculusMutation(s): 0 
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eS25
ZZ
75Oryctolagus cuniculusMutation(s): 0 
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eS26
aa
98Oryctolagus cuniculusMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
eS27
bb
83Oryctolagus cuniculusMutation(s): 0 
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eS28
cc
61Oryctolagus cuniculusMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetails
uS14
dd
53Oryctolagus cuniculusMutation(s): 0 
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eS30
ee
57Oryctolagus cuniculusMutation(s): 0 
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eS31
ff
69Oryctolagus cuniculusMutation(s): 0 
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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: 86
MoleculeChainsSequence LengthOrganismDetails
eRF1
ii
416Homo sapiensMutation(s): 2 
Gene Names: ERF1ETF1RF1SUP45L1
Find proteins for P62495 (Homo sapiens)
Go to UniProtKB:  P62495
NIH Common Fund Data Resources
PHAROS  P62495

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Entity ID: 87
MoleculeChainsSequence LengthOrganismDetails
ABCE1
jj
594Oryctolagus cuniculusMutation(s): 0 
Gene Names: ABCE1
Find proteins for G1SG72 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SG72

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Entity ID: 46
MoleculeChainsLengthOrganism
tRNA(Val)276Oryctolagus cuniculus

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Entity ID: 47
MoleculeChainsLengthOrganism
tRNA(Lys)375Oryctolagus cuniculus

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Entity ID: 48
MoleculeChainsLengthOrganism
28S ribosomal RNA53662Oryctolagus cuniculus

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Entity ID: 49
MoleculeChainsLengthOrganism
5S ribosomal RNA7120Oryctolagus cuniculus

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Entity ID: 50
MoleculeChainsLengthOrganism
5.8S ribosomal RNA8156Oryctolagus cuniculus

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Entity ID: 51
MoleculeChainsLengthOrganism
18S ribosomal RNA91719Oryctolagus cuniculus
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 85
MoleculeChainsLengthOrganism
mRNAhh12Oryctolagus cuniculus
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
jj
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
jj
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
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

Download CCD File 
5, 7, 8, 9, C, I, P, Q, V, g, hh
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



Entry History 

Deposition Data

Revision History 

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