Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 177035.58 
• Atom Count: 12396 
• Residue Count: 1588 
• Unique protein chains: 1

1D2E

CRYSTAL STRUCTURE OF MITOCHONDRIAL EF-TU IN COMPLEX WITH GDP

• DOI: 10.2210/pdb1D2E/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Bos taurus


• Deposited: 1999-09-23 Released: 1999-09-28 
• Deposition Author(s): Andersen, G.R., Thirup, S., Spremulli, L.L., Nyborg, J.

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Experimental Data Snapshot

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

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

• PubMed: 10715211 
• DOI: 10.1006/jmbi.2000.3564


• 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 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.

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Related Citations: 

• 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
• 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




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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
Molecule	Chains	Sequence Length	Organism	Details
ELONGATION FACTOR TU (EF-TU)	A, B, C, D	397	Bos taurus	Mutation(s): 0  Gene Names: TUFM
Find proteins for P49410 (Bos taurus) Go to Gene View: TUFM Go to UniProtKB:  P49410

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GDP	A, B, C, D	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GDP	Kd: 1000 nM BINDINGMOAD
GDP	Kd: 1000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.257 
• R-Value Work: 0.237 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 59.090	α = 90.00
b = 119.780	β = 96.97
c = 128.890	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
AMoRE	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-09-23 
• Released Date: 1999-09-28 
• Deposition Author(s): Andersen, G.R., Thirup, S., Spremulli, L.L., Nyborg, J.

Revision History 

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