3JCJ

Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association.

Sprink, T.Ramrath, D.J.Yamamoto, H.Yamamoto, K.Loerke, J.Ismer, J.Hildebrand, P.W.Scheerer, P.Burger, J.Mielke, T.Spahn, C.M.

(2016) Sci Adv 2: e1501502-e1501502

  • DOI: 10.1126/sciadv.1501502
  • Primary Citation of Related Structures:  
    3JCJ, 3JCN

  • PubMed Abstract: 
  • Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive ...

    Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAi (Met) in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.



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Translation initiation factor IF-2KA [auth f]890Escherichia coliMutation(s): 0 
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messenger RNAE [auth 4]52Escherichia coli
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tRNAZA [auth v]77Escherichia coli
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
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PG [auth f]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
FME
Query on FME

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SI [auth v]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
ZN
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OG [auth d]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
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AC [auth A] , AD [auth A] , AE [auth A] , AF [auth A] , AG [auth A] , AH [auth g] , AI [auth g] , BC [auth A] , 
AC [auth A],  AD [auth A],  AE [auth A],  AF [auth A],  AG [auth A],  AH [auth g],  AI [auth g],  BC [auth A],  BD [auth A],  BE [auth A],  BF [auth A],  BG [auth A],  BH [auth g],  BI [auth g],  CC [auth A],  CD [auth A],  CE [auth A],  CF [auth A],  CG [auth A],  CH [auth g],  CI [auth g],  DC [auth A],  DD [auth A],  DE [auth A],  DF [auth A],  DG [auth A],  DH [auth g],  DI [auth g],  EB [auth 3],  EC [auth A],  ED [auth A],  EE [auth A],  EF [auth A],  EG [auth A],  EH [auth g],  EI [auth g],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  FF [auth A],  FG [auth A],  FH [auth g],  FI [auth g],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  GF [auth A],  GG [auth A],  GH [auth g],  GI [auth g],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  HF [auth A],  HG [auth A],  HH [auth g],  HI [auth g],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  IF [auth A],  IG [auth A],  IH [auth g],  II [auth g],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  JF [auth A],  JG [auth A],  JH [auth g],  JI [auth g],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  KF [auth A],  KG [auth A],  KH [auth g],  KI [auth g],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  LF [auth A],  LG [auth A],  LH [auth g],  LI [auth g],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  MF [auth A],  MG [auth B],  MH [auth g],  MI [auth g],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  NF [auth A],  NG [auth d],  NH [auth g],  NI [auth g],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  OF [auth A],  OH [auth g],  OI [auth g],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth A],  PF [auth A],  PH [auth g],  PI [auth g],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth A],  QF [auth A],  QG [auth g],  QH [auth g],  QI [auth g],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth A],  RF [auth A],  RG [auth g],  RH [auth g],  RI [auth g],  SB [auth A],  SC [auth A],  SD [auth A],  SE [auth A],  SF [auth A],  SG [auth g],  SH [auth g],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth A],  TF [auth A],  TG [auth g],  TH [auth g],  TI [auth w],  UB [auth A],  UC [auth A],  UD [auth A],  UE [auth A],  UF [auth A],  UG [auth g],  UH [auth g],  VB [auth A],  VC [auth A],  VD [auth A],  VE [auth A],  VF [auth A],  VG [auth g],  VH [auth g],  WB [auth A],  WC [auth A],  WD [auth A],  WE [auth A],  WF [auth A],  WG [auth g],  WH [auth g],  XB [auth A],  XC [auth A],  XD [auth A],  XE [auth A],  XF [auth A],  XG [auth g],  XH [auth g],  YB [auth A],  YC [auth A],  YD [auth A],  YE [auth A],  YF [auth A],  YG [auth g],  YH [auth g],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZE [auth A],  ZF [auth A],  ZG [auth g],  ZH [auth g]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection