Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.41 kDa 
• Atom Count: 654 
• Modelled Residue Count: 654 
• Deposited Residue Count: 842 
• Unique protein chains: 1

3DNY

Fitting of the eEF2 crystal structure into the cryo-EM density map of the eEF2.80S.AlF4-.GDP complex

• PDB DOI: 10.2210/pdb3DNY/pdb
• EM Map EMD-5017:EMDBEMDataResource

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2008-07-03 Released: 2008-08-05 
• Deposition Author(s): Sengupta, J., Frank, J.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 12.6 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy.

Sengupta, J., Nilsson, J., Gursky, R., Kjeldgaard, M., Nissen, P., Frank, J.

(2008) J Mol Biol 382: 179-187

• PubMed: 18644383 
• DOI: 10.1016/j.jmb.2008.07.004
• Primary Citation of Related Structures:  
  3DNY, 3DWU


• PubMed Abstract: 
  

In an attempt to understand ribosome-induced GTP hydrolysis on eEF2, we determined a 12.6-A cryo-electron microscopy reconstruction of the eEF2-bound 80S ribosome in the presence of aluminum tetrafluoride and GDP, with aluminum tetrafluoride mimicking the gamma-phosphate during hydrolysis. This is the first visualization of a structure representing a transition-state complex on the ribosome. Tight interactions are observed between the factor's G domain and the large ribosomal subunit, as well as between domain IV and an intersubunit bridge. In contrast, some of the domains of eEF2 implicated in small subunit binding display a large degree of flexibility. Furthermore, we find support for a transition-state model conformation of the switch I region in this complex where the reoriented switch I region interacts with a conserved rRNA region of the 40S subunit formed by loops of the 18S RNA helices 8 and 14. This complex is structurally distinct from the eEF2-bound 80S ribosome complexes previously reported, and analysis of this map sheds light on the GTPase-coupled translocation mechanism.

---

Organizational Affiliation: 

Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 12.6 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-03 
• Released Date: 2008-08-05 
Deposition Author(s): Sengupta, J., Frank, J.

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-07-18
  Changes: Data collection