1JQS

Fitting of L11 protein and elongation factor G (domain G' and V) in the cryo-em map of E. coli 70S ribosome bound with EF-G and GMPPCP, a nonhydrolysable GTP analog


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 18 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

Localization of L11 protein on the ribosome and elucidation of its involvement in EF-G-dependent translocation.

Linde, J.Sengupta, J.Nierhaus, K.H.Frank, J.Agrawal, R.K.

(2001) J.Mol.Biol. 311: 777-787

  • DOI: 10.1006/jmbi.2001.4907
  • Primary Citation of Related Structures:  1JQM, 1JQT

  • PubMed Abstract: 
  • L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the 50 S subunit failed to locate the N-terminal domai ...

    L11 protein is located at the base of the L7/L12 stalk of the 50 S subunit of the Escherichia coli ribosome. Because of the flexible nature of the region, recent X-ray crystallographic studies of the 50 S subunit failed to locate the N-terminal domain of the protein. We have determined the position of the complete L11 protein by comparing a three-dimensional cryo-EM reconstruction of the 70 S ribosome, isolated from a mutant lacking ribosomal protein L11, with the three-dimensional map of the wild-type ribosome. Fitting of the X-ray coordinates of L11-23 S RNA complex and EF-G into the cryo-EM maps combined with molecular modeling, reveals that, following EF-G-dependent GTP hydrolysis, domain V of EF-G intrudes into the cleft between the 23 S ribosomal RNA and the N-terminal domain of L11 (where the antibiotic thiostrepton binds), causing the N-terminal domain to move and thereby inducing the formation of the arc-like connection with the G' domain of EF-G. The results provide a new insight into the mechanism of EF-G-dependent translocation.


    Related Citations: 
    • The Crystal Structure of Elongation Factor G Complexed with GDP, at 2.7A Resolution.
      Czworkowski, J.,Wang, J.,Steitz, T.A.,Moore, P.B.
      (1994) Embo J. 13: 3661
    • Structure of a Mutant EF-G Reveals Domain III and Possibly the Fusidic Acid Binding Site
      Laurberg, M.,Kristensen, O.,Martemyanov, K.,Gudkov, A.T.,Nagaev, I.,Hughes, D.,Liljas, A.
      (2000) J.Mol.Biol. 303: 593
    • EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
      Agrawal, R.K.,Heagle, A.B.,Penczek, P.,Grassucci, R.A.,Frank, J.
      (1999) Nat.Struct.Mol.Biol. 6: 643
    • Three-dimensional structure of the ribosomal translocase: Elongation factor G from Thermus thermophilus
      AEvarsson, A.,Brazhnikov, E.,Garber, M.,Zheltonosova, J.,Chirgadze, Y.,al-Karadaghi, S.,Svensson, L.A.,Liljas, A.
      (1994) Embo J. 13: 3669
    • A Detailed View of a Ribosomal Active Site: The Structure of the L11-RNA Complex
      Wimberly, B.T.,Guymon, R.,McCutcheon, J.P.,White, S.W.,Ramakrishnan, V.
      (1999) Cell 97: 491


    Organizational Affiliation

    Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA. agrawal@wadsworth.org




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal protein L11
A
139Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: rplK
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  P29395
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Elongation Factor G
B
32Thermus thermophilusGene Names: fusA (fus)
Find proteins for P13551 (Thermus thermophilus)
Go to UniProtKB:  P13551
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Elongation Factor G
C
68Thermus thermophilusGene Names: fusA (fus)
Find proteins for P13551 (Thermus thermophilus)
Go to UniProtKB:  P13551
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 18 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: 2001-09-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance