4PC2

Elongation factor Tu:Ts complex with a bound GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.

Thirup, S.S.Van, L.B.Nielsen, T.K.Knudsen, C.R.

(2015) J Struct Biol 191: 10-21

  • DOI: https://doi.org/10.1016/j.jsb.2015.06.011
  • Primary Citation of Related Structures:  
    4PC1, 4PC2, 4PC3, 4PC6, 4PC7

  • PubMed Abstract: 

    Translation elongation factor EF-Tu belongs to the superfamily of guanine-nucleotide binding proteins, which play key cellular roles as regulatory switches. All G-proteins require activation via exchange of GDP for GTP to carry out their respective tasks. Often, guanine-nucleotide exchange factors are essential to this process. During translation, EF-Tu:GTP transports aminoacylated tRNA to the ribosome. GTP is hydrolyzed during this process, and subsequent reactivation of EF-Tu is catalyzed by EF-Ts. The reaction path of guanine-nucleotide exchange is structurally poorly defined for EF-Tu and EF-Ts. We have determined the crystal structures of the following reaction intermediates: two structures of EF-Tu:GDP:EF-Ts (2.2 and 1.8Å resolution), EF-Tu:PO4:EF-Ts (1.9Å resolution), EF-Tu:GDPNP:EF-Ts (2.2Å resolution) and EF-Tu:GDPNP:pulvomycin:Mg(2+):EF-Ts (3.5Å resolution). These structures provide snapshots throughout the entire exchange reaction and suggest a mechanism for the release of EF-Tu in its GTP conformation. An inferred sequence of events during the exchange reaction is presented.


  • Organizational Affiliation

    Aarhus University, Department of Molecular Biology and Genetics, Center for Structural Biology, DK-8000 Aarhus C, Denmark. Electronic address: sth@mbg.au.dk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor TuA,
C [auth B]
394Escherichia coli str. K-12 substr. DH10BMutation(s): 0 
Gene Names: tufAtufECDH10B_3514
UniProt
Find proteins for A0A0M3KKV1 (Escherichia coli (strain K12 / DH10B))
Explore A0A0M3KKV1 
Go to UniProtKB:  A0A0M3KKV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KKV1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor TsB [auth C],
D
282Escherichia coliMutation(s): 0 
Gene Names: tsfBN17_45931ECs0172LF82_2325
UniProt
Find proteins for C3TPM7 (Escherichia coli)
Explore C3TPM7 
Go to UniProtKB:  C3TPM7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3TPM7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth C],
H [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C],
K [auth B],
L [auth B],
M [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.927α = 90
b = 108.51β = 90
c = 193.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2015-05-06 
  • Deposition Author(s): Thirup, S.S.

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references
  • Version 1.2: 2015-07-15
    Changes: Database references
  • Version 1.3: 2018-03-07
    Changes: Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description