4IOS

Structure of phage TP901-1 RBP (ORF49) in complex with nanobody 11.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Viral infection modulation and neutralization by camelid nanobodies

Desmyter, A.Farenc, C.Mahony, J.Spinelli, S.Bebeacua, C.Blangy, S.Veesler, D.van Sinderen, D.Cambillau, C.

(2013) Proc.Natl.Acad.Sci.USA 110: E1371-E1379

  • DOI: 10.1073/pnas.1301336110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lactococcal phages belong to a large family of Siphoviridae and infect Lactococcus lactis, a gram-positive bacterium used in commercial dairy fermentations. These phages are believed to recognize and bind specifically to pellicle polysaccharides cove ...

    Lactococcal phages belong to a large family of Siphoviridae and infect Lactococcus lactis, a gram-positive bacterium used in commercial dairy fermentations. These phages are believed to recognize and bind specifically to pellicle polysaccharides covering the entire bacterium. The phage TP901-1 baseplate, located at the tip of the tail, harbors 18 trimeric receptor binding proteins (RBPs) promoting adhesion to a specific lactococcal strain. Phage TP901-1 adhesion does not require major conformational changes or Ca(2+), which contrasts other lactococcal phages. Here, we produced and characterized llama nanobodies raised against the purified baseplate and the Tal protein of phage TP901-1 as tools to dissect the molecular determinants of phage TP901-1 infection. Using a set of complementary techniques, surface plasmon resonance, EM, and X-ray crystallography in a hybrid approach, we identified binders to the three components of the baseplate, analyzed their affinity for their targets, and determined their epitopes as well as their functional impact on TP901-1 phage infectivity. We determined the X-ray structures of three nanobodies in complex with the RBP. Two of them bind to the saccharide binding site of the RBP and are able to fully neutralize TP901-1 phage infectivity, even after 15 passages. These results provide clear evidence for a practical use of nanobodies in circumventing lactococcal phages viral infection in dairy fermentation.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 7257 Centre National de la Recherche Scientifique and Aix-Marseille University, 13288 Marseille Cedex 09, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BPP
A, B, C, H
100Lactococcus 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
Llama nanobody 11
D, E, F, G
123N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 148.280α = 90.00
b = 148.280β = 90.00
c = 104.590γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
MOLREPphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description