1LU3

Separate Fitting of the Anticodon Loop Region of tRNA (nucleotide 26-42) in the Low Resolution Cryo-EM Map of an EF-Tu Ternary Complex (GDP and Kirromycin) Bound to E. coli 70S Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 16.8 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

Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.

Valle, M.Sengupta, J.Swami, N.K.Grassucci, R.A.Burkhardt, N.Nierhaus, K.H.Agrawal, R.K.Frank, J.

(2002) EMBO J. 21: 3557-3567

  • DOI: 10.1093/emboj/cdf326
  • Primary Citation of Related Structures:  1LS2

  • PubMed Abstract: 
  • During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, ...

    During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, the anticodon end of the tRNA reaches the decoding center in the 30S subunit. Here we present the cryo- electron microscopy (EM) study of an Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic, kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new conformation that appears to facilitate the initial codon-anticodon interaction. Furthermore, the elbow region of the tRNA is seen to contact the GTPase-associated center on the 50S subunit of the ribosome, suggesting an active role of the tRNA in the transmission of the signal prompting the GTP hydrolysis upon codon recognition.


    Related Citations: 
    • Crystal structure of intact elongation factor EF-Tu from E.coli in GDP conformation at 2.05A resolution
      Song, H.,Parsons, M.R.,Rowsell, S.,Leonard, G.,Phillips, S.E.
      (1999) J.Mol.Biol. 285: 1245
    • The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation
      Kjeldgaard, M.,Nissen, P.,Thirup, S.,Nyborg, J.
      (1993) Structure 1: 35
    • Helix unwinding in the effector region of elongation factor EF-Tu-GDP
      Polekhina, G.,Thirup, S.,Kjeldgaard, M.,Nissen, P.,Lippmann, C.,Nyborg, J.
      (1996) Structure 4: 1141
    • Crystal structure of the ternary complex of the Phe-tRNAPhe, EF-Tu, and a GTP analog
      Nissen, P.,Kjeldgaard, M.,Thirup, S.,Polekhina, G.,Reshetnikova, L.,Clark, B.F.C.,Nyborg, J.
      (1995) Science 270: 1464
    • Visualization of elongation factor Tu on E.coli ribosome
      Stark, H.,Rodnina, M.V.,Rinke-Appel, J.,Brimacombe, R.,Wintermeyer, W.,van Heel, M.
      (1997) Nature 389: 403


    Organizational Affiliation

    Howard Hughes Medical Institute, Health Research, Inc., Empire State Plaza, Albany, NY 12201-0509, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
PHENYLALANINE TRANSFER RNAA17Saccharomyces cerevisiae
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A
RNA LINKINGC9 H13 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 16.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-26
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance