Structural biology

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The Structural Biology group operates a world leading suite of synchrotron radiation beamlines dedicated to the study of biological macromolecules:

Snapshots for the beamlines

 

 
Contacts
 

Gordon Leonard
SB Group Leader
+33 (0)4 76 88 23 94
email

     
 

 

Research highlights

Research performed at the ESRF produces over 20% of the protein structures submitted in the world and accounts for over 50% of those that come from Europe.  To see a list of structures solved at the ESRF see the BIOSYNC website. The following are some recent results.
 

Featured Highlight

 

Stuctural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors.

Boer et al, Cell 156, 577-589, January 30, 2014 

 

 Auxin is a plant hormone involved in key steps of growth, roots formation or flowering. The cellular response involves ubiquitin-proteasome dependent degradation of Auxin/Indole Acetic Acid (Aux/IAA) proteins, transcriptional corepressores that act by binding auxin response factors (ARFs). 

ARFs are modular transcription factors, consisting of four domains conserved in all members of this family. The DNA-Binding Domain (DBD) at the N-terminus, often followed by a Middle Region Domain that regulates transcription and C-terminal domain (III/IV) that mediates ARF-Aux/IAA interactions. 

ARF1-DBD.png

 

 

 

 

 

 

Figure 1- Crystal structure of ARF1-DBD monomer colored by subdomais (B3 DBD in green; DD in blue and yellow; AD in red).

 

The crystal structures of the DNA-binding domains of two different ARFs, ARF1 and ARF5, were determined on ID14-1 and ID14-4, at 1.45 Ȧ and 2.15 Ȧ resolution, respectively. ARF1-DBD was solved using single-wavelength anomalous dispersion (SAD) on a seleno-methionine (SeMet) derivative, and the resulting model was used for molecular replacement on the other structures.  

DBDs are composed of three structural sub-domains (figure 1). The binding domain B3, which folds in a seven-stranded beta-barrel structure, the dimerization domain DD, characterized by an antiparallel five-stranded central β-sheet that is highly curved (100o), resulting in a taco-like shape, and the anciliary domain AD  that folds in a small five-stranded β-barrel-like structure. ARF1 and ARF5 models subtly differed in the topology of several loops but showed the same overall structure. 

The dimer interface contacts of DD include hydrophobic interactions between several conserved aminoacids and stabilization by a network of hydrogen bonds. The authors used SAXS (BM29) to prove that dimerization was not just a crystallographic artifact and can occur in solution, as well. This dimerization revealed to be critical for in vivo ARF function. 

ARF1-DBD-ER7.png

 

 

 

 

 

 

Figure 2– Crystal structure of an ARF1-DBD/ER7 complex. ARF1-DBD monomers are differently colored. ER7 nucleotide sequence with auxin response elements (AuxRE) in orange.

 

The complex ARF1/DBD-DNA was cocrystallized and the structure solved at 2.9 Ȧ, on ID14-1. The complex has a U-shaped form with the DNA located on the tips of the dimer (figure 2). The two B3 domains bind to the inverted auxin response DNA elements located at both extremes of the oligonucleotide. Comparison between the structure apo- and DNA-bound ARF1-DBD didn't show huge differences, except the fact that the B3 domains are rotated relative to the DDs by 25o.  The loops that connect the B3 domain to the DD are mostly disorded in the structures, which indicates flexibility. This in agreement with the length differences in these loops on ARF1 and ARF5, suggests that this feature could be related with the ARF spacing preference/specificity.   

Link: http://www.cell.com/retrieve/pii/S0092867413015961

 

 

 

Introducing structural biology at the ESRF

 

Upgrade

The evolution of the facility, in the context of the ESRF upgrade, is encompassed within UPBL10/MASSIF.  This facility, to be located at beamlines ID30 and BM29, will have at its core three beamlines optimised for highly automated, high-throughput sample evaluation.

Industrial applications

Many of the world's leading pharmaceutical companies carry out proprietary research on our beamlines developing future drug candidates.  Industrial clients can access our facilities through our mail-in crystallography service MXpress or by applying directly for beamtime.  See the Industry website for details.

  

In-house research

In-house research runs in parallel to beamline operation, helping us to perfect techniques while investigating key scientific areas. Current projects include:

  • Beamline instrumentation (Kappa gonimeters, dehydration devices, sample characterisation)
  • The molecular basis of the extreme radiation resistance of Deinococcus radiodurans
  • Structural studies of enzymatic transition states
  • Activation mechanisms of LysR transcription regulators.

Additional details are in our Research & Development and Research Profiles pages.

 

Associated facilities

A number of laboratories and facilities are available to the community. Of particular interest is The Partnership for Structural Biology (PSB) which is a collaboration between ESRF, EMBL, ILL and IBS to bring together a set of complementary technologies for structural biology.

Collaborating Research Group beamlines

 

Locations

 
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More research highlights

View past highlights listing