6ORL

RF1 pre-accommodated 70S complex at 24 ms


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.

Fu, Z.Indrisiunaite, G.Kaledhonkar, S.Shah, B.Sun, M.Chen, B.Grassucci, R.A.Ehrenberg, M.Frank, J.

(2019) Nat Commun 10: 2579-2579

  • DOI: 10.1038/s41467-019-10608-z
  • Primary Citation of Related Structures:  
    6ORL, 6ORE, 6OT3, 6OST, 6OSK, 6OSQ, 6OUO

  • PubMed Abstract: 
  • When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away ...

    When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms.


    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY, 10027, USA. jf2192@cumc.columbia.edu.



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FME-PHE-PHEAB [auth H]3Escherichia coliMutation(s): 0 
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Peptide chain release factor 1BB [auth A]257Escherichia coliMutation(s): 0 
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23S ribosomal RNAA [auth 1]2903Escherichia coli
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    mRNACB [auth 4]9Escherichia coli
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    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

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    LM [auth f]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
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    Download Ideal Coordinates CCD File 
    AC [auth 1] , AD [auth 1] , AE [auth 1] , AF [auth 1] , AG [auth 1] , AH [auth 1] , AI [auth 1] , AJ [auth 1] , 
    AC [auth 1],  AD [auth 1],  AE [auth 1],  AF [auth 1],  AG [auth 1],  AH [auth 1],  AI [auth 1],  AJ [auth 1],  AK [auth 1],  AL [auth 1],  AM [auth 2],  BC [auth 1],  BD [auth 1],  BE [auth 1],  BF [auth 1],  BG [auth 1],  BH [auth 1],  BI [auth 1],  BJ [auth 1],  BK [auth 1],  BL [auth 1],  BM [auth 3],  CC [auth 1],  CD [auth 1],  CE [auth 1],  CF [auth 1],  CG [auth 1],  CH [auth 1],  CI [auth 1],  CJ [auth 1],  CK [auth 1],  CL [auth 1],  CM [auth 3],  DB [auth 1],  DC [auth 1],  DD [auth 1],  DE [auth 1],  DF [auth 1],  DG [auth 1],  DH [auth 1],  DI [auth 1],  DJ [auth 1],  DK [auth 1],  DL [auth 1],  DM [auth 3],  EB [auth 1],  EC [auth 1],  ED [auth 1],  EE [auth 1],  EF [auth 1],  EG [auth 1],  EH [auth 1],  EI [auth 1],  EJ [auth 1],  EK [auth 1],  EL [auth 1],  EM [auth 3],  FB [auth 1],  FC [auth 1],  FD [auth 1],  FE [auth 1],  FF [auth 1],  FG [auth 1],  FH [auth 1],  FI [auth 1],  FJ [auth 1],  FK [auth 1],  FL [auth 1],  FM [auth 3],  GB [auth 1],  GC [auth 1],  GD [auth 1],  GE [auth 1],  GF [auth 1],  GG [auth 1],  GH [auth 1],  GI [auth 1],  GJ [auth 1],  GK [auth 1],  GL [auth 1],  GM [auth 3],  HB [auth 1],  HC [auth 1],  HD [auth 1],  HE [auth 1],  HF [auth 1],  HG [auth 1],  HH [auth 1],  HI [auth 1],  HJ [auth 1],  HK [auth 1],  HL [auth 1],  HM [auth 3],  IB [auth 1],  IC [auth 1],  ID [auth 1],  IE [auth 1],  IF [auth 1],  IG [auth 1],  IH [auth 1],  II [auth 1],  IJ [auth 1],  IK [auth 1],  IL [auth 1],  IM [auth 3],  JB [auth 1],  JC [auth 1],  JD [auth 1],  JE [auth 1],  JF [auth 1],  JG [auth 1],  JH [auth 1],  JI [auth 1],  JJ [auth 1],  JK [auth 1],  JL [auth 1],  JM [auth C],  KB [auth 1],  KC [auth 1],  KD [auth 1],  KE [auth 1],  KF [auth 1],  KG [auth 1],  KH [auth 1],  KI [auth 1],  KJ [auth 1],  KK [auth 1],  KL [auth 1],  KM [auth b],  LB [auth 1],  LC [auth 1],  LD [auth 1],  LE [auth 1],  LF [auth 1],  LG [auth 1],  LH [auth 1],  LI [auth 1],  LJ [auth 1],  LK [auth 1],  LL [auth 1],  MB [auth 1],  MC [auth 1],  MD [auth 1],  ME [auth 1],  MF [auth 1],  MG [auth 1],  MH [auth 1],  MI [auth 1],  MJ [auth 1],  MK [auth 1],  ML [auth 1],  MM [auth i],  NB [auth 1],  NC [auth 1],  ND [auth 1],  NE [auth 1],  NF [auth 1],  NG [auth 1],  NH [auth 1],  NI [auth 1],  NJ [auth 1],  NK [auth 1],  NL [auth 1],  OB [auth 1],  OC [auth 1],  OD [auth 1],  OE [auth 1],  OF [auth 1],  OG [auth 1],  OH [auth 1],  OI [auth 1],  OJ [auth 1],  OK [auth 1],  OL [auth 1],  PB [auth 1],  PC [auth 1],  PD [auth 1],  PE [auth 1],  PF [auth 1],  PG [auth 1],  PH [auth 1],  PI [auth 1],  PJ [auth 1],  PK [auth 1],  PL [auth 1],  QB [auth 1],  QC [auth 1],  QD [auth 1],  QE [auth 1],  QF [auth 1],  QG [auth 1],  QH [auth 1],  QI [auth 1],  QJ [auth 1],  QK [auth 1],  QL [auth 1],  RB [auth 1],  RC [auth 1],  RD [auth 1],  RE [auth 1],  RF [auth 1],  RG [auth 1],  RH [auth 1],  RI [auth 1],  RJ [auth 1],  RK [auth 1],  RL [auth 1],  SB [auth 1],  SC [auth 1],  SD [auth 1],  SE [auth 1],  SF [auth 1],  SG [auth 1],  SH [auth 1],  SI [auth 1],  SJ [auth 1],  SK [auth 1],  SL [auth 1],  TB [auth 1],  TC [auth 1],  TD [auth 1],  TE [auth 1],  TF [auth 1],  TG [auth 1],  TH [auth 1],  TI [auth 1],  TJ [auth 1],  TK [auth 1],  TL [auth 1],  UB [auth 1],  UC [auth 1],  UD [auth 1],  UE [auth 1],  UF [auth 1],  UG [auth 1],  UH [auth 1],  UI [auth 1],  UJ [auth 1],  UK [auth 1],  UL [auth 1],  VB [auth 1],  VC [auth 1],  VD [auth 1],  VE [auth 1],  VF [auth 1],  VG [auth 1],  VH [auth 1],  VI [auth 1],  VJ [auth 1],  VK [auth 1],  VL [auth 1],  WB [auth 1],  WC [auth 1],  WD [auth 1],  WE [auth 1],  WF [auth 1],  WG [auth 1],  WH [auth 1],  WI [auth 1],  WJ [auth 1],  WK [auth 1],  WL [auth 1],  XB [auth 1],  XC [auth 1],  XD [auth 1],  XE [auth 1],  XF [auth 1],  XG [auth 1],  XH [auth 1],  XI [auth 1],  XJ [auth 1],  XK [auth 1],  XL [auth 1],  YB [auth 1],  YC [auth 1],  YD [auth 1],  YE [auth 1],  YF [auth 1],  YG [auth 1],  YH [auth 1],  YI [auth 1],  YJ [auth 1],  YK [auth 1],  YL [auth 1],  ZB [auth 1],  ZC [auth 1],  ZD [auth 1],  ZE [auth 1],  ZF [auth 1],  ZG [auth 1],  ZH [auth 1],  ZI [auth 1],  ZJ [auth 1],  ZK [auth 1],  ZL [auth 1]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  2 Unique
    IDChainsTypeFormula2D DiagramParent
    0TD
    Query on 0TD
    PA [auth q]L-PEPTIDE LINKINGC5 H9 N O4 SASP
    FME
    Query on FME
    AB [auth H]L-PEPTIDE LINKINGC6 H11 N O3 SMET
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.50 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM55440
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29169
    Swedish Research CouncilSweden--

    Revision History  (Full details and data files)

    • Version 1.0: 2019-06-19
      Type: Initial release
    • Version 1.1: 2019-06-26
      Changes: Data collection, Database references
    • Version 1.2: 2019-12-18
      Changes: Author supporting evidence, Other