1EFT | pdb_00001eft

THE CRYSTAL STRUCTURE OF ELONGATION FACTOR EF-TU FROM THERMUS AQUATICUS IN THE GTP CONFORMATION

• PDB DOI: https://doi.org/10.2210/pdb1EFT/pdb

• Classification: ELONGATION FACTOR
• Organism(s): Thermus aquaticus
• Mutation(s): No 


• Deposited: 1993-08-24 Released: 1994-08-31 
• Deposition Author(s): Kjeldgaard, M., Nissen, P., Thirup, S., Nyborg, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.200 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation.

Kjeldgaard, M., Nissen, P., Thirup, S., Nyborg, J.

(1993) Structure 1: 35-50

• PubMed: 8069622 
• DOI: https://doi.org/10.1016/0969-2126(93)90007-4
• Primary Citation Related Structures: 
  1EFT


• PubMed Abstract: 
  

  Elongation factor Tu (EF-Tu) is a GTP-binding protein that is crucial for protein biosynthesis. In the GTP form of the molecule, EF-Tu binds tightly to aminoacyl-tRNA, forming a ternary complex that interacts with the ribosomal acceptor site. During this interaction, GTP is hydrolyzed, and EF-Tu.GDP is ejected. The crystal structure of EF-Tu from Thermus aquaticus, complexed to the GTP analogue GDPNP, has been determined at 2.5 A resolution and compared to the structure of Escherichia coli EF-Tu.GDP. During the transition from the GDP (inactive) to the GTP (active) form, domain 1, containing the GTP-binding site, undergoes internal conformational changes similar to those observed in ras-p21. In addition, a dramatic rearrangement of domains is observed, corresponding to a rotation of 90.8 degrees of domain 1 relative to domains 2 and 3. Residues that are affected in the binding of aminoacyl-tRNA are found in or near the cleft formed by the domain interface. GTP binding by EF-Tu leads to dramatic conformational changes which expose the tRNA binding site. It appears that tRNA binding to EF-Tu induces a further conformational change, which may affect the GTPase activity.

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Organizational Affiliation: 
• Department of Chemistry, Aarhus University, Denmark.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.28 kDa 
• Atom Count: 3,302 
• Modeled Residue Count: 405 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELONGATION FACTOR TU	A	405	Thermus aquaticus	Mutation(s): 0  EC: 3.6.5.3
UniProt
Find proteins for Q01698 (Thermus aquaticus) Explore Q01698  Go to UniProtKB:  Q01698

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.200 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.7	α = 90
b = 99.7	β = 95.3
c = 40.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-08-31 
Deposition Author(s): Kjeldgaard, M., Nissen, P., Thirup, S., Nyborg, J.

Revision History  

• Version 1.0: 1994-08-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other