1N0U

Crystal structure of yeast elongation factor 2 in complex with sordarin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase.

Jorgensen, R., Ortiz, P.A., Carr-Schmid, A., Nissen, P., Kinzy, T.G., Andersen, G.R.

(2003) Nat Struct Biol 10: 379-385

  • DOI: 10.1038/nsb923
  • Primary Citation of Related Structures:  
    1N0V, 1N0U

  • PubMed Abstract: 

    • Two crystal structures of yeast translation elongation factor 2 (eEF2) were determined: the apo form at 2.9 A resolution and eEF2 in the presence of the translocation inhibitor sordarin at 2.1 A resolution. The overall conformation of apo eEF2 is similar to that of its prokaryotic homolog elongation factor G (EF-G) in complex with GDP ...

    Two crystal structures of yeast translation elongation factor 2 (eEF2) were determined: the apo form at 2.9 A resolution and eEF2 in the presence of the translocation inhibitor sordarin at 2.1 A resolution. The overall conformation of apo eEF2 is similar to that of its prokaryotic homolog elongation factor G (EF-G) in complex with GDP. Upon sordarin binding, the three tRNA-mimicking C-terminal domains undergo substantial conformational changes, while the three N-terminal domains containing the nucleotide-binding site form an almost rigid unit. The conformation of eEF2 in complex with sordarin is entirely different from known conformations observed in crystal structures of EF-G or from cryo-EM studies of EF-G-70S complexes. The domain rearrangements induced by sordarin binding and the highly ordered drug-binding site observed in the eEF2-sordarin structure provide a high-resolution structural basis for the mechanism of sordarin inhibition. The two structures also emphasize the dynamic nature of the ribosomal translocase.

    Related Citations: 
    • Purification and Crystallization of the yeast elongation factor eEF2
      Joergensen, R., Carr-Schmid, A., Ortiz, P.A., Kinzy, T.G., Andersen, G.R.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 712
    Organizational Affiliation: 

    Department of Molecular Biology, Aarhus University, Gustav Wieds vej 10C, DK8000 Arhus, Denmark.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 2A842Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32324 
Go to UniProtKB:  P32324
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO1
Query on SO1
Download Ideal Coordinates CCD File 
 B [auth A][1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID
C27 H42 O8
DIBGPTPYRVEPSP-OHFCZZTFSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.96α = 90
b = 150.83β = 90
c = 65.07γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
CNSrefinement
CCP4data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-12-20
    Changes: Database references
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation