Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 377.48 kDa 
• Atom Count: 24874 
• Residue Count: 3385 
• Unique protein chains: 2

3NOG

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

• DOI: 10.2210/pdb3NOG/pdb

• Classification: TRANSPORT PROTEIN/PROTEIN BINDING
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-25 Released: 2011-05-18 
• Deposition Author(s): Monroe, N., Briand, C., Gruetter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.34 Å
• R-Value Free: 0.307 
• R-Value Work: 0.257 
• R-Value Observed: 0.258 

Literature

Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface

Monroe, N., Sennhauser, G., Seeger, M.A., Briand, C., Grutter, M.G.

(2011) J Struct Biol 174: 269-281

• PubMed: 21296164 
• DOI: 10.1016/j.jsb.2011.01.014
• Primary Citation of Related Structures:  
  3NOG, 3NOC


• 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.

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Organizational Affiliation: 

Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acriflavine resistance protein B	A, B, C	1049	Escherichia coli K-12	Mutation(s): 0  Gene Names: acrB, acrE, b0462, JW0451
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed ankyrin repeat protein	D, E	169	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	A,B,C	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.34 Å
• R-Value Free: 0.307 
• R-Value Work: 0.257 
• R-Value Observed: 0.258 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.4	α = 90
b = 158	β = 90
c = 258.6	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-25 
• Released Date: 2011-05-18 
Deposition Author(s): Monroe, N., Briand, C., Gruetter, M.G.

Revision History 

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance