3JAH

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 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: https://doi.org/10.1038/nature14896
  • Primary Citation of Related Structures:  
    3JAG, 3JAH, 3JAI

  • 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 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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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
uL2244Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL3394Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL4362Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL18292Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SYJ6 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eL6248Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL30225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eL8241Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL6190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL16213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL5169Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eL13K [auth L]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eL14L [auth M]138Oryctolagus cuniculusMutation(s): 0 
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Find proteins for U3KNW6 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eL15M [auth N]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL13N [auth O]199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL22O [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uL14P [auth Q]187Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL19Q [auth R]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eL20R [auth S]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL21S [auth T]159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL22T [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uL14U [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL24V [auth W]63Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL23W [auth X]119Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL24X [auth Y]134Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eL27Y [auth Z]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uL15Z [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL29AA [auth b]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eL30BA [auth c]94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eL31CA [auth d]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eL32DA [auth e]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eL33EA [auth f]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL34FA [auth g]114Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U945 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uL29GA [auth h]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL36HA [auth i]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL37IA [auth j]86Oryctolagus cuniculusMutation(s): 0 
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Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL38JA [auth k]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL39KA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SYU7 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL40LA [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eL41MA [auth n]23Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL42NA [auth o]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
eL43OA [auth p]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL28PA [auth r]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
uL10QA [auth s]198Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
uL11RA [auth t]163Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
peptideSA [auth 1]15Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
uS2ZA [auth AA]208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
eS1AB [auth BB]213Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
uS5BB [auth CC]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
uS3CB [auth DD]227Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
eS4DB [auth EE]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
uS7EB [auth FF]191Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
eS6FB [auth GG]237Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
eS7GB [auth HH]189Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
eS8HB [auth II]206Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
uS4IB [auth JJ]185Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
eS10JB [auth KK]98Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPV3 (Oryctolagus cuniculus)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
uS17KB [auth LL]152Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
eS12LB [auth MM]124Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uS15MB [auth NN]150Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uS11NB [auth OO]136Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T1F0 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
uS19OB [auth PP]127Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
uS9PB [auth QQ]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
eS17QB [auth RR]129Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
uS13RB [auth SS]137Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZI5 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
eS19SB [auth TT]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
uS10TB [auth UU]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
eS21UB [auth VV]83Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
uS8VB [auth WW]129Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
uS12WB [auth XX]141Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
eS24XB [auth YY]126Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
eS25YB [auth ZZ]75Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
eS26ZB [auth aa]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
eS27AC [auth bb]83Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
eS28BC [auth cc]61Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
uS14CC [auth dd]53Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
eS30DC [auth ee]57Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
eS31EC [auth ff]68Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1FC [auth gg]313Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
eRF1HC [auth ii]416Homo sapiensMutation(s): 2 
Gene Names: eRF1
UniProt & NIH Common Fund Data Resources
Find proteins for P62495 (Homo sapiens)
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PHAROS:  P62495
GTEx:  ENSG00000120705 
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
ABCE1IC [auth jj]594Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SG72 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains LengthOrganismImage
tRNA(Val)TA [auth 2]76Oryctolagus cuniculus
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Entity ID: 47
MoleculeChains LengthOrganismImage
tRNA(Lys)UA [auth 3]75Oryctolagus cuniculus
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Entity ID: 48
MoleculeChains LengthOrganismImage
28S ribosomal RNAVA [auth 5]3,662Oryctolagus cuniculus
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Entity ID: 49
MoleculeChains LengthOrganismImage
5S ribosomal RNAWA [auth 7]120Oryctolagus cuniculus
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Entity ID: 50
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAXA [auth 8]156Oryctolagus cuniculus
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Entity ID: 51
MoleculeChains LengthOrganismImage
18S ribosomal RNAYA [auth 9]1,719Oryctolagus cuniculus
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Entity ID: 85
MoleculeChains LengthOrganismImage
mRNAGC [auth hh]12Oryctolagus cuniculus
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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GK [auth jj],
HK [auth jj]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4
Query on SF4

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EK [auth jj],
FK [auth jj]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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AK [auth aa]
BK [auth dd]
CK [auth ff]
OC [auth g]
QC [auth j]
AK [auth aa],
BK [auth dd],
CK [auth ff],
OC [auth g],
QC [auth j],
RC [auth m],
SC [auth o],
TC [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AD [auth 5]
AE [auth 5]
AF [auth 5]
AG [auth 5]
AH [auth 5]
AD [auth 5],
AE [auth 5],
AF [auth 5],
AG [auth 5],
AH [auth 5],
AI [auth 5],
AJ [auth 9],
BD [auth 5],
BE [auth 5],
BF [auth 5],
BG [auth 5],
BH [auth 5],
BI [auth 5],
BJ [auth 9],
CD [auth 5],
CE [auth 5],
CF [auth 5],
CG [auth 5],
CH [auth 5],
CI [auth 5],
CJ [auth 9],
DD [auth 5],
DE [auth 5],
DF [auth 5],
DG [auth 5],
DH [auth 5],
DI [auth 5],
DJ [auth 9],
DK [auth hh],
ED [auth 5],
EE [auth 5],
EF [auth 5],
EG [auth 5],
EH [auth 5],
EI [auth 5],
EJ [auth 9],
FD [auth 5],
FE [auth 5],
FF [auth 5],
FG [auth 5],
FH [auth 5],
FI [auth 5],
FJ [auth 9],
GD [auth 5],
GE [auth 5],
GF [auth 5],
GG [auth 5],
GH [auth 5],
GI [auth 5],
GJ [auth 9],
HD [auth 5],
HE [auth 5],
HF [auth 5],
HG [auth 5],
HH [auth 5],
HI [auth 5],
HJ [auth 9],
ID [auth 5],
IE [auth 5],
IF [auth 5],
IG [auth 5],
IH [auth 5],
II [auth 5],
IJ [auth 9],
JC [auth B],
JD [auth 5],
JE [auth 5],
JF [auth 5],
JG [auth 5],
JH [auth 5],
JI [auth 5],
JJ [auth 9],
KC [auth C],
KD [auth 5],
KE [auth 5],
KF [auth 5],
KG [auth 5],
KH [auth 5],
KI [auth 7],
KJ [auth 9],
LC [auth I],
LD [auth 5],
LE [auth 5],
LF [auth 5],
LG [auth 5],
LH [auth 5],
LI [auth 7],
LJ [auth 9],
MC [auth P],
MD [auth 5],
ME [auth 5],
MF [auth 5],
MG [auth 5],
MH [auth 5],
MI [auth 7],
MJ [auth 9],
NC [auth V],
ND [auth 5],
NE [auth 5],
NF [auth 5],
NG [auth 5],
NH [auth 5],
NI [auth 7],
NJ [auth 9],
OD [auth 5],
OE [auth 5],
OF [auth 5],
OG [auth 5],
OH [auth 5],
OI [auth 7],
OJ [auth 9],
PC [auth g],
PD [auth 5],
PE [auth 5],
PF [auth 5],
PG [auth 5],
PH [auth 5],
PI [auth 8],
PJ [auth 9],
QD [auth 5],
QE [auth 5],
QF [auth 5],
QG [auth 5],
QH [auth 5],
QI [auth 8],
QJ [auth 9],
RD [auth 5],
RE [auth 5],
RF [auth 5],
RG [auth 5],
RH [auth 5],
RI [auth 9],
RJ [auth 9],
SD [auth 5],
SE [auth 5],
SF [auth 5],
SG [auth 5],
SH [auth 5],
SI [auth 9],
SJ [auth 9],
TD [auth 5],
TE [auth 5],
TF [auth 5],
TG [auth 5],
TH [auth 5],
TI [auth 9],
TJ [auth 9],
UC [auth 5],
UD [auth 5],
UE [auth 5],
UF [auth 5],
UG [auth 5],
UH [auth 5],
UI [auth 9],
UJ [auth 9],
VC [auth 5],
VD [auth 5],
VE [auth 5],
VF [auth 5],
VG [auth 5],
VH [auth 5],
VI [auth 9],
VJ [auth 9],
WC [auth 5],
WD [auth 5],
WE [auth 5],
WF [auth 5],
WG [auth 5],
WH [auth 5],
WI [auth 9],
WJ [auth 9],
XC [auth 5],
XD [auth 5],
XE [auth 5],
XF [auth 5],
XG [auth 5],
XH [auth 5],
XI [auth 9],
XJ [auth 9],
YC [auth 5],
YD [auth 5],
YE [auth 5],
YF [auth 5],
YG [auth 5],
YH [auth 5],
YI [auth 9],
YJ [auth 9],
ZC [auth 5],
ZD [auth 5],
ZE [auth 5],
ZF [auth 5],
ZG [auth 5],
ZH [auth 5],
ZI [auth 9],
ZJ [auth LL]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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