2E1R

Structure of eEF2 in complex with a sordarin derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2

Soe, R.Mosley, R.T.Justice, M.Nielsen-Kahn, J.Shastry, M.Merrill, A.R.Andersen, G.R.

(2007) J.Biol.Chem. 282: 657-666

  • DOI: 10.1074/jbc.M607830200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The sordarins are fungal specific inhibitors of the translation factor eEF2, which catalyzes the translocation of tRNA and mRNA after peptide bond formation. We have determined the crystal structures of eEF2 in complex with two novel sordarin derivat ...

    The sordarins are fungal specific inhibitors of the translation factor eEF2, which catalyzes the translocation of tRNA and mRNA after peptide bond formation. We have determined the crystal structures of eEF2 in complex with two novel sordarin derivatives. In both structures, the three domains of eEF2 that form the ligand-binding pocket are oriented in a different manner relative to the rest of eEF2 compared with our previous structure of eEF2 in complex with the parent natural product sordarin. Yeast eEF2 is also shown to bind adenylic nucleotides, which can be displaced by sordarin, suggesting that ADP or ATP also bind to the three C-terminal domains of eEF2. Fusidic acid is a universal inhibitor of translation that targets EF-G or eEF2 and is widely used as an antibiotic against Gram-positive bacteria. Based on mutations conferring resistance to fusidic acid, cryo-EM reconstructions, and x-ray structures of eEF2, EF-G, and an EF-G homolog, we suggest that the conformation of EF-G stalled on the 70 S ribosome by fusidic acid is similar to that of eEF2 trapped on the 80 S ribosome by sordarin.


    Organizational Affiliation

    Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus C, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor 2
A
842Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: EFT1, EFT2
Find proteins for P32324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32324
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SOD
Query on SOD

Download SDF File 
Download CCD File 
A
(1S,4S,5S,6R,9S,11S)-6-CHLORO-9-FORMYL-13-ISOPROPYL-5-METHYL-2-({[(3AR,5R,7R ,7AS)-7-METHYL-3-METHYLENEHEXAHYDRO-2H-FURO[2,3-C]PYRAN-5-YL]OXY}METHYL)TETR ACYCLO[7.4.0.02,11.04,8]TRIDEC-12-ENE-1-CARBOXYLIC ACI
C29 H39 Cl O6
OFLZRRPTCKISFB-SHWNUAPTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 116.860α = 90.00
b = 158.770β = 90.00
c = 60.310γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MAR345data collection
MOLREPphasing
XDSdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description