3NOG

Designed ankyrin repeat protein (DARPin) Binders to AcrB: Plasticity of the Interface

Summary for 3NOG

• Entry DOI: 10.2210/pdb3nog/pdb
• Related: 2J8S 3NOC
• Descriptor: Acriflavine resistance protein B, Designed ankyrin repeat protein (2 entities in total)
• Functional Keywords: membrane protein, rnd, drug-efflux pump, transport protein, designed ankyrin repeat protein, crystallization chaperone, transport protein-protein binding complex, transport protein/protein binding
• Biological source: Escherichia coli; More
• Cellular location: Cell inner membrane; Multi-pass membrane protein: P31224
• Total number of polymer chains: 5
• Total formula weight: 377482.14

Authors

Monroe, N.,Briand, C.,Gruetter, M.G. (deposition date: 2010-06-25, release date: 2011-05-18, Last modification date: 2024-11-06)

Primary citation

Monroe, N.,Sennhauser, G.,Seeger, M.A.,Briand, C.,Grutter, M.G.
Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface
J.Struct.Biol., 174:269-281, 2011

PubMed Abstract: The formation of well-diffracting crystals is a major bottleneck in structural analysis of membrane proteins by X-ray crystallography. One approach to improve crystal quality is the use of DARPins as crystallization chaperones. Here, we present a detailed analysis of the interaction between DARPins and the integral membrane protein AcrB. We find that binders selected in vitro by ribosome display share a common epitope. The comparative analysis of three crystal structures of AcrB-DARPin complexes allowed us to study the plasticity of the interaction with this dominant binding site. Seemingly redundant AcrB-DARPin crystals show substantially different diffraction quality as a result of subtle differences in the binding geometry. This work exemplifies the importance to screen a number of crystallization chaperones to obtain optimal diffraction data. Crystallographic analysis is complemented by biophysical characterization of nine AcrB binders. We observe that small variations in the interface can lead to differing behavior of the DARPins with regards to affinity, stoichiometry of the complexes and specificity for their target.

PubMed: 21296164
DOI: 10.1016/j.jsb.2011.01.014

Experimental method

X-RAY DIFFRACTION (3.34 Å)