1TTT

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

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 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 angstro ...

    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.

    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

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
OF ELONGATION FACTOR TU (EF-TU)
A, B, C
405Thermus aquaticusMutation(s): 0 
Gene Names: tuf (tufA)
Find proteins for Q01698 (Thermus aquaticus)
Go to UniProtKB:  Q01698
Entity ID: 1
MoleculeChainsLengthOrganism
TRANSFER RIBONUCLEIC ACID (YEAST, PHE)D,E,F76N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE
Download SDF File 
Download CCD File 
D, E, F
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP
Download SDF File 
Download CCD File 
A, B, C
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
D, E, F
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
D, E, F
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
D, E, F
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
D, E, F
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
D, E, F
RNA LINKINGC10 H16 N3 O8 PC
YYG
Query on YYG
D, E, F
RNA LINKINGC21 H29 N6 O12 PG
2MG
Query on 2MG
D, E, F
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
D, E, F
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
D, E, F
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
D, E, F
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
D, E, F
RNA LINKINGC9 H15 N2 O9 PU
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 = 206.835α = 90.00
b = 122.354β = 126.30
c = 151.552γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

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