1D2E

CRYSTAL STRUCTURE OF MITOCHONDRIAL EF-TU IN COMPLEX WITH GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High resolution crystal structure of bovine mitochondrial EF-Tu in complex with GDP.

Andersen, G.R.Thirup, S.Spremulli, L.L.Nyborg, J.

(2000) J Mol Biol 297: 421-436

  • DOI: 10.1006/jmbi.2000.3564
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of bovine mitochondrial elongation factor Tu (EF-Tu) in complex with GDP has been determined at a resolution of 1. 94 A. The structure is similar to that of EF-Tu:GDP from Escherichia coli and Thermus aquaticus, but the orientat ...

    The crystal structure of bovine mitochondrial elongation factor Tu (EF-Tu) in complex with GDP has been determined at a resolution of 1. 94 A. The structure is similar to that of EF-Tu:GDP from Escherichia coli and Thermus aquaticus, but the orientation of the GDP-binding domain 1 is changed relative to domains 2 and 3. Sixteen conserved water molecules common to EF-Tu and other G-proteins in the GDP-binding site are described. These water molecules create a network linking separated parts of the binding pocket. Mitochondrial EF-Tu binds nucleotides less tightly than prokaryotic EF-Tu possibly due to an increased mobility in regions close to the GDP-binding site. The C-terminal extension of mitochondrial EF-Tu has structural similarities with DNA recognising zinc fingers suggesting that the extension may be involved in recognition of RNA.


    Related Citations: 
    • Crystal Structure of Intact Elongation Factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A Resolution
      Song, H., Parsons, M.R., Rowsell, S., Leonard, G., Phillips, S.E.V.
      (1999) J Mol Biol 285: 1245
    • Helix Unwinding in the Effector Region of Elongation Factor EF-Tu-GDP
      Polekhina, G., Thirup, S., Kjeldgaard, M., Nissen, P., Lippmann, C., Nyborg, J.
      (1996) Structure 4: 1141

    Organizational Affiliation

    Institute of Molecular and Structural Biology, Aarhus University, Gustav Wiedsvej 10C, Aarhus, DK8000, Denmark.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELONGATION FACTOR TU (EF-TU)A, B, C, D397Bos taurusMutation(s): 0 
Gene Names: TUFM
Find proteins for P49410 (Bos taurus)
Explore P49410 
Go to UniProtKB:  P49410
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download CCD File 
A, B, C, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GDPKd :  1000   nM  PDBBind
GDPKd:  1000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.09α = 90
b = 119.78β = 96.97
c = 128.89γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation