Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.90 kDa 
• Atom Count: 6904 
• Modelled Residue Count: 819 
• Deposited Residue Count: 842 
• Unique protein chains: 1

1N0U

Crystal structure of yeast elongation factor 2 in complex with sordarin

• PDB DOI: 10.2210/pdb1N0U/pdb

• Classification: TRANSLATION
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2002-10-15 Released: 2003-02-11 
• Deposition Author(s): Joergensen, R., Ortiz, P.A., Carr-Schmid, A., Nissen, P., Kinzy, T.G., Andersen, G.R.

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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 

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

• PubMed: 12692531 
• DOI: 10.1038/nsb923
• Primary Citation of Related Structures:  
  1N0U, 1N0V


• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor 2	A	842	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32324  Go to UniProtKB:  P32324

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO1	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

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 = 119.96	α = 90
b = 150.83	β = 90
c = 65.07	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELXD	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-15 
• Released Date: 2003-02-11 
Deposition Author(s): Joergensen, R., Ortiz, P.A., Carr-Schmid, A., Nissen, P., Kinzy, T.G., Andersen, G.R.

Revision History  

• 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