3JAI

Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA 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:  
    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 ...

    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.



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uL2A244Oryctolagus cuniculusMutation(s): 0 
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uL3B394Oryctolagus cuniculusMutation(s): 0 
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uL4C361Oryctolagus cuniculusMutation(s): 0 
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EC: 4.2.99.18
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
eS21UB [auth VV]83Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
Find proteins for G1TM82 (Oryctolagus cuniculus)
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Entity ID: 74
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uS8VB [auth WW]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
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uS12WB [auth XX]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
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eS24XB [auth YY]126Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
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eS25YB [auth ZZ]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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eS26ZB [auth aa]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
eS27AC [auth bb]83Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
eS28BC [auth cc]61Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
uS14CC [auth dd]53Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
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eS30DC [auth ee]57Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
eS31EC [auth ff]68Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
RACK1FC [auth gg]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetailsImage
eRF1HC [auth ii]416Homo sapiensMutation(s): 2 
Gene Names: ERF1ETF1RF1SUP45L1
Find proteins for P62495 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS:  P62495
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Entity ID: 87
MoleculeChainsSequence LengthOrganismDetailsImage
ABCE1IC [auth jj]594Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChainsLengthOrganismImage
tRNA(Val)TA [auth 2]76Oryctolagus cuniculus
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Entity ID: 47
MoleculeChainsLengthOrganismImage
tRNA(Lys)UA [auth 3]75Oryctolagus cuniculus
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Entity ID: 48
MoleculeChainsLengthOrganismImage
28S ribosomal RNAVA [auth 5]3662Oryctolagus cuniculus
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Entity ID: 49
MoleculeChainsLengthOrganismImage
5S ribosomal RNAWA [auth 7]120Oryctolagus cuniculus
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Entity ID: 50
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAXA [auth 8]156Oryctolagus cuniculus
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Entity ID: 51
MoleculeChainsLengthOrganismImage
18S ribosomal RNAYA [auth 9]1719Oryctolagus cuniculus
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  • Entity ID: 85
    MoleculeChainsLengthOrganismImage
    mRNAGC [auth hh]12Oryctolagus cuniculus
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    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP

    Download Ideal Coordinates CCD File 
    GK [auth jj], HK [auth jj]ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    SF4
    Query on SF4

    Download Ideal Coordinates CCD File 
    EK [auth jj], FK [auth jj]IRON/SULFUR CLUSTER
    Fe4 S4
    LJBDFODJNLIPKO-VKOJMFJBAC
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    AK [auth aa], BK [auth dd], CK [auth ff], NC [auth g], PC [auth j], QC [auth m], RC [auth o], SC [auth p]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AD [auth 5] , AE [auth 5] , AF [auth 5] , AG [auth 5] , AH [auth 5] , AI [auth 5] , AJ [auth 9] , BD [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 C],  JD [auth 5],  JE [auth 5],  JF [auth 5],  JG [auth 5],  JH [auth 5],  JI [auth 5],  JJ [auth 9],  KC [auth I],  KD [auth 5],  KE [auth 5],  KF [auth 5],  KG [auth 5],  KH [auth 5],  KI [auth 7],  KJ [auth 9],  LC [auth P],  LD [auth 5],  LE [auth 5],  LF [auth 5],  LG [auth 5],  LH [auth 5],  LI [auth 7],  LJ [auth 9],  MC [auth V],  MD [auth 5],  ME [auth 5],  MF [auth 5],  MG [auth 5],  MH [auth 5],  MI [auth 7],  MJ [auth 9],  ND [auth 5],  NE [auth 5],  NF [auth 5],  NG [auth 5],  NH [auth 5],  NI [auth 7],  NJ [auth 9],  OC [auth g],  OD [auth 5],  OE [auth 5],  OF [auth 5],  OG [auth 5],  OH [auth 5],  OI [auth 7],  OJ [auth 9],  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],  TC [auth 5],  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 9]
    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  (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