6GZ4

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-2 (TI-POST-2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.

Flis, J.Holm, M.Rundlet, E.J.Loerke, J.Hilal, T.Dabrowski, M.Burger, J.Mielke, T.Blanchard, S.C.Spahn, C.M.T.Budkevich, T.V.

(2018) Cell Rep 25: 2676-2688.e7

  • DOI: 10.1016/j.celrep.2018.11.040
  • Primary Citation of Related Structures:  
    6GZ4, 6GZ3, 6GZ5

  • PubMed Abstract: 
  • Translocation moves the tRNA 2 ⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated ...

    Translocation moves the tRNA 2 ⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA 2 ⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address: tetyana.budkevych@charite.de.



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ribosomal protein uL2A [auth AA]252Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS2B [auth BA]215Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL3C [auth AB]394Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS1D [auth BB]212Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uL4E [auth AC]363Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS28F [auth BC]222Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS3L [auth BD]220Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS7M [auth BF]190Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS10N [auth BK]98Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eS12O [auth BM]120Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS19P [auth BP]120Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL36VB [auth Ai]97Oryctolagus cuniculusMutation(s): 0 
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eukaryotic elongation factor 2 (eEF2)HC [auth Ct]853Oryctolagus cuniculusMutation(s): 0 
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28S ribosomal RNAG [auth A2]3612Oryctolagus cuniculus
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ap/P-site tRNAH [auth Bv]76Oryctolagus cuniculus
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    mRNAI [auth Bx]11Oryctolagus cuniculus
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    18S ribosomal RNAK [auth B1]1708Oryctolagus cuniculus
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    5.8S ribosomal RNAPA [auth A3]157Oryctolagus cuniculus
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    5S ribosomal RNAQA [auth A4]119Oryctolagus cuniculus
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    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GNP
    Query on GNP

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    CP [auth Ct]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    AP [auth Ao], BP [auth Ap], HO [auth Bd], JO [auth Ba], YO [auth Aj]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AD [auth A2] , AE [auth A2] , AF [auth A2] , AG [auth A2] , AH [auth A2] , AI [auth A2] , AJ [auth A2] , AK [auth A2] , 
    AD [auth A2],  AE [auth A2],  AF [auth A2],  AG [auth A2],  AH [auth A2],  AI [auth A2],  AJ [auth A2],  AK [auth A2],  AL [auth A2],  AM [auth B1],  AN [auth B1],  AO [auth B1],  BD [auth A2],  BE [auth A2],  BF [auth A2],  BG [auth A2],  BH [auth A2],  BI [auth A2],  BJ [auth A2],  BK [auth A2],  BL [auth A2],  BM [auth B1],  BN [auth B1],  BO [auth BD],  CD [auth A2],  CE [auth A2],  CF [auth A2],  CG [auth A2],  CH [auth A2],  CI [auth A2],  CJ [auth A2],  CK [auth A2],  CL [auth A2],  CM [auth B1],  CN [auth B1],  CO [auth BD],  DD [auth A2],  DE [auth A2],  DF [auth A2],  DG [auth A2],  DH [auth A2],  DI [auth A2],  DJ [auth A2],  DK [auth A2],  DL [auth A2],  DM [auth B1],  DN [auth B1],  DO [auth BS],  ED [auth A2],  EE [auth A2],  EF [auth A2],  EG [auth A2],  EH [auth A2],  EI [auth A2],  EJ [auth A2],  EK [auth A2],  EL [auth A2],  EM [auth B1],  EN [auth B1],  EO [auth BS],  FD [auth A2],  FE [auth A2],  FF [auth A2],  FG [auth A2],  FH [auth A2],  FI [auth A2],  FJ [auth A2],  FK [auth A2],  FL [auth A2],  FM [auth B1],  FN [auth B1],  FO [auth Bd],  GD [auth A2],  GE [auth A2],  GF [auth A2],  GG [auth A2],  GH [auth A2],  GI [auth A2],  GJ [auth A2],  GK [auth A2],  GL [auth A2],  GM [auth B1],  GN [auth B1],  GO [auth Bd],  HD [auth A2],  HE [auth A2],  HF [auth A2],  HG [auth A2],  HH [auth A2],  HI [auth A2],  HJ [auth A2],  HK [auth A2],  HL [auth A2],  HM [auth B1],  HN [auth B1],  IC [auth AA],  ID [auth A2],  IE [auth A2],  IF [auth A2],  IG [auth A2],  IH [auth A2],  II [auth A2],  IJ [auth A2],  IK [auth A2],  IL [auth A2],  IM [auth B1],  IN [auth B1],  IO [auth Ba],  JC [auth A2],  JD [auth A2],  JE [auth A2],  JF [auth A2],  JG [auth A2],  JH [auth A2],  JI [auth A2],  JJ [auth A2],  JK [auth A2],  JL [auth A2],  JM [auth B1],  JN [auth B1],  KC [auth A2],  KD [auth A2],  KE [auth A2],  KF [auth A2],  KG [auth A2],  KH [auth A2],  KI [auth A2],  KJ [auth A2],  KK [auth A2],  KL [auth A2],  KM [auth B1],  KN [auth B1],  KO [auth A3],  LC [auth A2],  LD [auth A2],  LE [auth A2],  LF [auth A2],  LG [auth A2],  LH [auth A2],  LI [auth A2],  LJ [auth A2],  LK [auth A2],  LL [auth Bx],  LM [auth B1],  LN [auth B1],  LO [auth A3],  MC [auth A2],  MD [auth A2],  ME [auth A2],  MF [auth A2],  MG [auth A2],  MH [auth A2],  MI [auth A2],  MJ [auth A2],  MK [auth A2],  ML [auth B1],  MM [auth B1],  MN [auth B1],  MO [auth A3],  NC [auth A2],  ND [auth A2],  NE [auth A2],  NF [auth A2],  NG [auth A2],  NH [auth A2],  NI [auth A2],  NJ [auth A2],  NK [auth A2],  NL [auth B1],  NM [auth B1],  NN [auth B1],  NO [auth A3],  OC [auth A2],  OD [auth A2],  OE [auth A2],  OF [auth A2],  OG [auth A2],  OH [auth A2],  OI [auth A2],  OJ [auth A2],  OK [auth A2],  OL [auth B1],  OM [auth B1],  ON [auth B1],  OO [auth A4],  PC [auth A2],  PD [auth A2],  PE [auth A2],  PF [auth A2],  PG [auth A2],  PH [auth A2],  PI [auth A2],  PJ [auth A2],  PK [auth A2],  PL [auth B1],  PM [auth B1],  PN [auth B1],  PO [auth A4],  QC [auth A2],  QD [auth A2],  QE [auth A2],  QF [auth A2],  QG [auth A2],  QH [auth A2],  QI [auth A2],  QJ [auth A2],  QK [auth A2],  QL [auth B1],  QM [auth B1],  QN [auth B1],  QO [auth A4],  RC [auth A2],  RD [auth A2],  RE [auth A2],  RF [auth A2],  RG [auth A2],  RH [auth A2],  RI [auth A2],  RJ [auth A2],  RK [auth A2],  RL [auth B1],  RM [auth B1],  RN [auth B1],  RO [auth A4],  SC [auth A2],  SD [auth A2],  SE [auth A2],  SF [auth A2],  SG [auth A2],  SH [auth A2],  SI [auth A2],  SJ [auth A2],  SK [auth A2],  SL [auth B1],  SM [auth B1],  SN [auth B1],  SO [auth A4],  TC [auth A2],  TD [auth A2],  TE [auth A2],  TF [auth A2],  TG [auth A2],  TH [auth A2],  TI [auth A2],  TJ [auth A2],  TK [auth A2],  TL [auth B1],  TM [auth B1],  TN [auth B1],  TO [auth A4],  UC [auth A2],  UD [auth A2],  UE [auth A2],  UF [auth A2],  UG [auth A2],  UH [auth A2],  UI [auth A2],  UJ [auth A2],  UK [auth A2],  UL [auth B1],  UM [auth B1],  UN [auth B1],  UO [auth A4],  VC [auth A2],  VD [auth A2],  VE [auth A2],  VF [auth A2],  VG [auth A2],  VH [auth A2],  VI [auth A2],  VJ [auth A2],  VK [auth A2],  VL [auth B1],  VM [auth B1],  VN [auth B1],  VO [auth A4],  WC [auth A2],  WD [auth A2],  WE [auth A2],  WF [auth A2],  WG [auth A2],  WH [auth A2],  WI [auth A2],  WJ [auth A2],  WK [auth A2],  WL [auth B1],  WM [auth B1],  WN [auth B1],  WO [auth AL],  XC [auth A2],  XD [auth A2],  XE [auth A2],  XF [auth A2],  XG [auth A2],  XH [auth A2],  XI [auth A2],  XJ [auth A2],  XK [auth A2],  XL [auth B1],  XM [auth B1],  XN [auth B1],  XO [auth AY],  YC [auth A2],  YD [auth A2],  YE [auth A2],  YF [auth A2],  YG [auth A2],  YH [auth A2],  YI [auth A2],  YJ [auth A2],  YK [auth A2],  YL [auth B1],  YM [auth B1],  YN [auth B1],  ZC [auth A2],  ZD [auth A2],  ZE [auth A2],  ZF [auth A2],  ZG [auth A2],  ZH [auth A2],  ZI [auth A2],  ZJ [auth A2],  ZK [auth A2],  ZL [auth B1],  ZM [auth B1],  ZN [auth B1],  ZO [auth An]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    DDE
    Query on DDE
    HC [auth Ct]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.60 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    German Research FoundationGermanyDFG SFB 740
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM079238
    National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM115327-Tan

    Revision History  (Full details and data files)

    • Version 1.0: 2018-12-05
      Type: Initial release
    • Version 1.1: 2018-12-19
      Changes: Data collection, Database references
    • Version 2.0: 2019-02-06
      Changes: Atomic model, Data collection, Derived calculations