5LZT

Structure of the mammalian ribosomal termination complex with eRF1 and eRF3.


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 1.3 of the entry. See complete history


Literature

Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes.

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

(2016) Cell 167: 1229-1240.e15

  • DOI: 10.1016/j.cell.2016.10.046
  • Primary Citation of Related Structures:  
    5LZT, 5LZS, 5LZV, 5LZU, 5LZX, 5LZW, 5LZZ, 5LZY

  • PubMed Abstract: 
  • In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the mammalian ribosome engaged with decoding factor⋅GTPase complexes representing intermediates of translation elongation (aminoacyl-tRNA⋅eEF1A), termination (eRF1⋅eRF3), and ribosome rescue (Pelota⋅Hbs1l) ...

    In eukaryotes, accurate protein synthesis relies on a family of translational GTPases that pair with specific decoding factors to decipher the mRNA code on ribosomes. We present structures of the mammalian ribosome engaged with decoding factor⋅GTPase complexes representing intermediates of translation elongation (aminoacyl-tRNA⋅eEF1A), termination (eRF1⋅eRF3), and ribosome rescue (Pelota⋅Hbs1l). Comparative analyses reveal that each decoding factor exploits the plasticity of the ribosomal decoding center to differentially remodel ribosomal proteins and rRNA. This leads to varying degrees of large-scale ribosome movements and implies distinct mechanisms for communicating information from the decoding center to each GTPase. Additional structural snapshots of the translation termination pathway reveal the conformational changes that choreograph the accommodation of decoding factors into the peptidyl transferase center. Our results provide a structural framework for how different states of the mammalian ribosome are selectively recognized by the appropriate decoding factor⋅GTPase complex to ensure translational fidelity.


    Related Citations: 
    • Decoding mammalian ribosome-mRNA states by translational GTPase complexes
      Shao, S., Murray, J., Brown, A., Taunton, J., Ramakrishnan, V., Hegde, R.S.
      () To be published --: --

    Organizational Affiliation

    MRC-LMB, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: rhegde@mrc-lmb.cam.ac.uk.



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Entity ID: 1
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uL2A257Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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uL3B403Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
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uL4C425Oryctolagus cuniculusMutation(s): 0 
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uL18D297Oryctolagus cuniculusMutation(s): 0 
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eL6E291Oryctolagus cuniculusMutation(s): 0 
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uL30F247Oryctolagus cuniculusMutation(s): 0 
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eL14L [auth M]218Oryctolagus cuniculusMutation(s): 0 
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uL22O [auth P]184Oryctolagus cuniculusMutation(s): 0 
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eL24V [auth W]157Oryctolagus cuniculusMutation(s): 0 
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eL29AA [auth b]245Oryctolagus cuniculusMutation(s): 0 
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eL39KA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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eL42NA [auth o]106Oryctolagus cuniculusMutation(s): 0 
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Nascent chainSA [auth 1]15Oryctolagus cuniculusMutation(s): 0 
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uS2ZA [auth AA]295Oryctolagus cuniculusMutation(s): 0 
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eS1AB [auth BB]264Oryctolagus cuniculusMutation(s): 0 
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uS3CB [auth DD]243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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uS7EB [auth FF]204Oryctolagus cuniculusMutation(s): 0 
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eS8HB [auth II]208Oryctolagus cuniculusMutation(s): 0 
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eS10JB [auth KK]165Oryctolagus cuniculusMutation(s): 0 
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uS17KB [auth LL]158Oryctolagus cuniculusMutation(s): 0 
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uS15MB [auth NN]151Oryctolagus cuniculusMutation(s): 0 
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uS11NB [auth OO]168Oryctolagus cuniculusMutation(s): 0 
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uS19OB [auth PP]145Oryctolagus cuniculusMutation(s): 0 
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uS9PB [auth QQ]146Oryctolagus cuniculusMutation(s): 0 
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uS13RB [auth SS]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
uS10TB [auth UU]119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
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eS21UB [auth VV]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
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uS8VB [auth WW]130Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 75
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uS12WB [auth XX]143Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
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eS24XB [auth YY]130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
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eS25YB [auth ZZ]125Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 78
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eS26ZB [auth aa]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
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eS27AC [auth bb]84Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 80
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eS28BC [auth cc]69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 81
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uS14CC [auth dd]56Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 82
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eS30DC [auth ee]133Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 83
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eS31EC [auth ff]156Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
RACK1FC [auth gg]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetailsImage
eRF1HC [auth ii]459Homo sapiensMutation(s): 0 
Gene Names: ETF1ERF1RF1SUP45L1
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
eRF3aIC [auth jj]637Homo sapiensMutation(s): 0 
Gene Names: GSPT1ERF3A
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Entity ID: 46
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P-site tRNATA [auth 2]76Oryctolagus cuniculus
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Entity ID: 47
MoleculeChainsLengthOrganismImage
E-site tRNAUA [auth 3]75Oryctolagus cuniculus
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Entity ID: 48
MoleculeChainsLengthOrganismImage
28S ribosomal RNAVA [auth 5]3543Oryctolagus cuniculus
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Entity ID: 49
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5S ribosomal RNAWA [auth 7]120Oryctolagus cuniculus
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Entity ID: 50
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5.8S ribosomal RNAXA [auth 8]156Oryctolagus cuniculus
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Entity ID: 51
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18S ribosomal RNAYA [auth 9]1869Oryctolagus cuniculus
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  • Entity ID: 85
    MoleculeChainsLengthOrganismImage
    mRNA (UGA stop codon)GC [auth hh]15Oryctolagus cuniculus
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    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GCP
    Query on GCP

    Download Ideal Coordinates CCD File 
    MN [auth jj]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
    C11 H18 N5 O13 P3
    PHBDHXOBFUBCJD-KQYNXXCUSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    IN [auth aa], JN [auth dd], KN [auth ff], SC [auth g], UC [auth j], WC [auth m], XC [auth o], YC [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 5] , AK [auth 5] , 
    AD [auth 5],  AE [auth 5],  AF [auth 5],  AG [auth 5],  AH [auth 5],  AI [auth 5],  AJ [auth 5],  AK [auth 5],  AL [auth 9],  AM [auth 9],  AN [auth 9],  BD [auth 5],  BE [auth 5],  BF [auth 5],  BG [auth 5],  BH [auth 5],  BI [auth 5],  BJ [auth 5],  BK [auth 5],  BL [auth 9],  BM [auth 9],  BN [auth 9],  CD [auth 5],  CE [auth 5],  CF [auth 5],  CG [auth 5],  CH [auth 5],  CI [auth 5],  CJ [auth 5],  CK [auth 7],  CL [auth 9],  CM [auth 9],  CN [auth 9],  DD [auth 5],  DE [auth 5],  DF [auth 5],  DG [auth 5],  DH [auth 5],  DI [auth 5],  DJ [auth 5],  DK [auth 7],  DL [auth 9],  DM [auth 9],  DN [auth 9],  ED [auth 5],  EE [auth 5],  EF [auth 5],  EG [auth 5],  EH [auth 5],  EI [auth 5],  EJ [auth 5],  EK [auth 7],  EL [auth 9],  EM [auth 9],  EN [auth 9],  FD [auth 5],  FE [auth 5],  FF [auth 5],  FG [auth 5],  FH [auth 5],  FI [auth 5],  FJ [auth 5],  FK [auth 7],  FL [auth 9],  FM [auth 9],  FN [auth 9],  GD [auth 5],  GE [auth 5],  GF [auth 5],  GG [auth 5],  GH [auth 5],  GI [auth 5],  GJ [auth 5],  GK [auth 7],  GL [auth 9],  GM [auth 9],  GN [auth 9],  HD [auth 5],  HE [auth 5],  HF [auth 5],  HG [auth 5],  HH [auth 5],  HI [auth 5],  HJ [auth 5],  HK [auth 8],  HL [auth 9],  HM [auth 9],  HN [auth 9],  ID [auth 5],  IE [auth 5],  IF [auth 5],  IG [auth 5],  IH [auth 5],  II [auth 5],  IJ [auth 5],  IK [auth 8],  IL [auth 9],  IM [auth 9],  JC [auth A],  JD [auth 5],  JE [auth 5],  JF [auth 5],  JG [auth 5],  JH [auth 5],  JI [auth 5],  JJ [auth 5],  JK [auth 8],  JL [auth 9],  JM [auth 9],  KC [auth B],  KD [auth 5],  KE [auth 5],  KF [auth 5],  KG [auth 5],  KH [auth 5],  KI [auth 5],  KJ [auth 5],  KK [auth 8],  KL [auth 9],  KM [auth 9],  LC [auth I],  LD [auth 5],  LE [auth 5],  LF [auth 5],  LG [auth 5],  LH [auth 5],  LI [auth 5],  LJ [auth 5],  LK [auth 8],  LL [auth 9],  LM [auth 9],  LN [auth hh],  MC [auth P],  MD [auth 5],  ME [auth 5],  MF [auth 5],  MG [auth 5],  MH [auth 5],  MI [auth 5],  MJ [auth 5],  MK [auth 8],  ML [auth 9],  MM [auth 9],  NC [auth P],  ND [auth 5],  NE [auth 5],  NF [auth 5],  NG [auth 5],  NH [auth 5],  NI [auth 5],  NJ [auth 5],  NK [auth 8],  NL [auth 9],  NM [auth 9],  NN [auth jj],  OC [auth P],  OD [auth 5],  OE [auth 5],  OF [auth 5],  OG [auth 5],  OH [auth 5],  OI [auth 5],  OJ [auth 5],  OK [auth 8],  OL [auth 9],  OM [auth 9],  PC [auth Q],  PD [auth 5],  PE [auth 5],  PF [auth 5],  PG [auth 5],  PH [auth 5],  PI [auth 5],  PJ [auth 5],  PK [auth 9],  PL [auth 9],  PM [auth 9],  QC [auth V],  QD [auth 5],  QE [auth 5],  QF [auth 5],  QG [auth 5],  QH [auth 5],  QI [auth 5],  QJ [auth 5],  QK [auth 9],  QL [auth 9],  QM [auth 9],  RC [auth a],  RD [auth 5],  RE [auth 5],  RF [auth 5],  RG [auth 5],  RH [auth 5],  RI [auth 5],  RJ [auth 5],  RK [auth 9],  RL [auth 9],  RM [auth 9],  SD [auth 5],  SE [auth 5],  SF [auth 5],  SG [auth 5],  SH [auth 5],  SI [auth 5],  SJ [auth 5],  SK [auth 9],  SL [auth 9],  SM [auth 9],  TC [auth g],  TD [auth 5],  TE [auth 5],  TF [auth 5],  TG [auth 5],  TH [auth 5],  TI [auth 5],  TJ [auth 5],  TK [auth 9],  TL [auth 9],  TM [auth 9],  UD [auth 5],  UE [auth 5],  UF [auth 5],  UG [auth 5],  UH [auth 5],  UI [auth 5],  UJ [auth 5],  UK [auth 9],  UL [auth 9],  UM [auth 9],  VC [auth j],  VD [auth 5],  VE [auth 5],  VF [auth 5],  VG [auth 5],  VH [auth 5],  VI [auth 5],  VJ [auth 5],  VK [auth 9],  VL [auth 9],  VM [auth 9],  WD [auth 5],  WE [auth 5],  WF [auth 5],  WG [auth 5],  WH [auth 5],  WI [auth 5],  WJ [auth 5],  WK [auth 9],  WL [auth 9],  WM [auth 9],  XD [auth 5],  XE [auth 5],  XF [auth 5],  XG [auth 5],  XH [auth 5],  XI [auth 5],  XJ [auth 5],  XK [auth 9],  XL [auth 9],  XM [auth 9],  YD [auth 5],  YE [auth 5],  YF [auth 5],  YG [auth 5],  YH [auth 5],  YI [auth 5],  YJ [auth 5],  YK [auth 9],  YL [auth 9],  YM [auth 9],  ZC [auth 5],  ZD [auth 5],  ZE [auth 5],  ZF [auth 5],  ZG [auth 5],  ZH [auth 5],  ZI [auth 5],  ZJ [auth 5],  ZK [auth 9],  ZL [auth 9],  ZM [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 & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Medical Research Council (United Kingdom)United KingdomMC_UP_A022_1007
    Medical Research Council (United Kingdom)United KingdomMC_U105184332
    Wellcome TrustUnited KingdomWT096570

    Revision History  (Full details and data files)

    • Version 1.0: 2016-11-30
      Type: Initial release
    • Version 1.1: 2017-08-30
      Changes: Author supporting evidence, Data collection, Derived calculations
    • Version 1.2: 2018-10-10
      Changes: Data collection, Refinement description, Structure summary
    • Version 1.3: 2019-12-11
      Changes: Other, Structure summary