Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 211107.28 
• Atom Count: 14523 
• Residue Count: 1443 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1TTT

Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex

• DOI: 10.2210/pdb1TTT/pdb
• NDB: PTR012

• Classification: COMPLEX (ELONGATION FACTOR/TRNA)
• Organism(s): Thermus aquaticus


• Deposited: 1995-11-16 Released: 1996-12-23 
• Deposition Author(s): Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B.F.C., Nyborg, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.290 
• R-Value Work: 0.206 

Literature

Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog.

Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B.F., Nyborg, J.

(1995) Science 270: 1464-1472

• PubMed: 7491491 


• PubMed Abstract: 
  

The structure of the ternary complex consisting of yeast phenylalanyl-transfer RNA (Phe-tRNAPhe), Thermus aquaticus elongation factor Tu (EF-Tu), and the guanosine triphosphate (GTP) analog GDPNP was determined by x-ray crystallography at 2.7 angstrom resolution. The ternary complex participates in placing the amino acids in their correct order when messenger RNA is translated into a protein sequence on the ribosome. The EF-Tu-GDPNP component binds to one side of the acceptor helix of Phe-tRNAPhe involving all three domains of EF-Tu. Binding sites for the phenylalanylated CCA end and the phosphorylated 5' end are located at domain interfaces, whereas the T stem interacts with the surface of the beta-barrel domain 3. The binding involves many conserved residues in EF-Tu. The overall shape of the ternary complex is similar to that of the translocation factor, EF-G-GDP, and this suggests a novel mechanism involving "molecular mimicry" in the translational apparatus.

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Related Citations: 

• 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
• Purification and Crystallization of the Ternary Complex of Elongation Factor TU:GTP and Phe-tRNA(Phe)
  Nissen, P.,Reshetnikova, L.,Siboska, G.,Polekhina, G.,Thirup, S.,Kjeldgaard, M.,Clark, B.F.,Nyborg, J.
  (1994) FEBS Lett. 356: 165




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Organizational Affiliation: 

Department of Biostructural Chemistry, Institute of Chemistry, Aarhus University, Denmark.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
OF ELONGATION FACTOR TU (EF-TU)	A, B, C	405	Thermus aquaticus	Mutation(s): 0  Gene Names: tuf (tufA)
Find proteins for Q01698 (Thermus aquaticus) Go to UniProtKB:  Q01698

Entity ID: 1
Molecule	Chains	Length	Organism
TRANSFER RIBONUCLEIC ACID (YEAST, PHE)	D,E,F	76	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PHE	D, E, F	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
MG	A, B, C, D, E, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
GNP	A, B, C	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N

Modified Residues  11 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PSU	D, E, F	RNA LINKING	C9 H13 N2 O9 P		U
5MC	D, E, F	RNA LINKING	C10 H16 N3 O8 P		C
M2G	D, E, F	RNA LINKING	C12 H18 N5 O8 P		G
1MA	D, E, F	RNA LINKING	C11 H16 N5 O7 P		A
OMC	D, E, F	RNA LINKING	C10 H16 N3 O8 P		C
YYG	D, E, F	RNA LINKING	C21 H29 N6 O12 P		G
2MG	D, E, F	RNA LINKING	C11 H16 N5 O8 P		G
OMG	D, E, F	RNA LINKING	C11 H16 N5 O8 P		G
7MG	D, E, F	RNA LINKING	C11 H18 N5 O8 P		G
5MU	D, E, F	RNA LINKING	C10 H15 N2 O9 P		U
H2U	D, E, F	RNA LINKING	C9 H15 N2 O9 P		U

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.290 
• R-Value Work: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 206.835	α = 90.00
b = 122.354	β = 126.30
c = 151.552	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-11-16 
• Released Date: 1996-12-23 
• Deposition Author(s): Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B.F.C., Nyborg, J.

Revision History 

• Version 1.0: 1996-12-23
  Type: Initial release
• Version 1.1: 2008-05-22
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance