3HG0

Crystal structure of a DARPin in complex with ORF49 from Lactococcal phage TP901-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and function of a DARPin neutralizing inhibitor of lactococcal phage TP901-1: comparison of DARPin and camelid VHH binding mode.

Veesler, D.Dreier, B.Blangy, S.Lichiere, J.Tremblay, D.Moineau, S.Spinelli, S.Tegoni, M.Pluckthun, A.Campanacci, V.Cambillau, C.

(2009) J.Biol.Chem. 284: 30718-30726

  • DOI: 10.1074/jbc.M109.037812

  • PubMed Abstract: 
  • Combinatorial libraries of designed ankyrin repeat proteins (DARPins) have been proven to be a valuable source of specific binding proteins, as they can be expressed at very high levels and are very stable. We report here the selection of DARPins dir ...

    Combinatorial libraries of designed ankyrin repeat proteins (DARPins) have been proven to be a valuable source of specific binding proteins, as they can be expressed at very high levels and are very stable. We report here the selection of DARPins directed against a macromolecular multiprotein complex, the baseplate BppUxBppL complex of the lactococcal phage TP901-1. Using ribosome display, we selected several DARPins that bound specifically to the tip of the receptor-binding protein (RBP, the BppL trimer). The three selected DARPins display high specificity and affinity in the low nanomolar range and bind with a stoichiometry of one DARPin per BppL trimer. The crystal structure of a DARPin complexed with the RBP was solved at 2.1 A resolution. The DARPinxRBP interface is of the concave (DARPin)-convex (RBP) type, typical of other DARPin protein complexes and different from what is observed with a camelid VHH domain, which penetrates the phage p2 RBP inter-monomer interface. Finally, phage infection assays demonstrated that TP901-1 infection of Lactococcus lactis cells was inhibited by each of the three selected DARPins. This study provides proof of concept for the possible use of DARPins to circumvent viral infection. It also provides support for the use of DARPins in co-crystallization, due to their rigidity and their ability to provide multiple crystal contacts.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and the Universités Aix-Marseille I and II, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baseplate protein
A, B, C
169Lactococcus phage TP901-1Mutation(s): 0 
Gene Names: bpp
Find proteins for Q9G096 (Lactococcus phage TP901-1)
Go to UniProtKB:  Q9G096
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Designed Ankyrin Repeat Protein (DARPin) 20
D
136N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.650α = 90.00
b = 80.440β = 90.00
c = 182.870γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
AMoREphasing
PHENIXrefinement
XDSdata reduction
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-09-25
    Type: Derived calculations