3EP2

Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9 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

Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.

Li, W.Agirrezabala, X.Lei, J.Bouakaz, L.Brunelle, J.L.Ortiz-Meoz, R.F.Green, R.Sanyal, S.Ehrenberg, M.Frank, J.

(2008) Embo J. 27: 3322-3331

  • DOI: 10.1038/emboj.2008.243
  • Primary Citation of Related Structures:  3EQ3, 3EQ4

  • PubMed Abstract: 
  • The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes of different aa-tRNAs, we compared cryo-EM maps of ...

    The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes of different aa-tRNAs, we compared cryo-EM maps of the kirromycin-stalled ribosome bound with ternary complexes containing Phe-tRNA(Phe), Trp-tRNA(Trp), or Leu-tRNA(LeuI). The three maps suggest a common binding manner of cognate aa-tRNAs in their specific binding with both the ribosome and EF-Tu. All three aa-tRNAs have the same 'loaded spring' conformation with a kink and twist between the D-stem and anticodon stem. The three complexes are similarly integrated in an interaction network, extending from the anticodon loop through h44 and protein S12 to the EF-Tu-binding CCA end of aa-tRNA, proposed to signal cognate codon-anticodon interaction to the GTPase centre and tune the accuracy of aa-tRNA selection.


    Related Citations: 
    • Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy
      Valle, M.,Zavialov, A.,Li, W.,Stagg, S.M.,Sengupta, J.,Nielsen, R.C.,Nissen, P.,Harvey, S.C.,Ehrenberg, M.,Frank, J.
      (2003) Nat. Struct. Molec. Biol. 10: 899


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu
X
393Escherichia coli (strain K12)Gene Names: tufB
Find proteins for P0CE48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE48
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
123Escherichia coli (strain K12)Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
141Escherichia coli (strain K12)Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 4
MoleculeChainsLengthOrganism
tRNAY74Escherichia coli K-12
Entity ID: 5
MoleculeChainsLengthOrganism
Fragment h18 of the 16S rRNAA9Escherichia coli K-12
Entity ID: 6
MoleculeChainsLengthOrganism
Fragment h44 of the 16S rRNAC11Escherichia coli K-12
Entity ID: 7
MoleculeChainsLengthOrganism
Fragment H43-44 of the 23S rRNAB48Escherichia coli K-12
Entity ID: 8
MoleculeChainsLengthOrganism
Fragment H95 of the 23S rRNAD28Escherichia coli K-12
Entity ID: 9
MoleculeChainsLengthOrganism
Fragment H69 of the 23S rRNAE17Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9 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: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-05-30
    Type: Refinement description