5E7F

Complex between lactococcal phage Tuc2009 RBP head domain and a nanobody (L06)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules.

Legrand, P.Collins, B.Blangy, S.Murphy, J.Spinelli, S.Gutierrez, C.Richet, N.Kellenberger, C.Desmyter, A.Mahony, J.van Sinderen, D.Cambillau, C.

(2016) mBio 7: e01781-e01715

  • DOI: 10.1128/mBio.01781-15
  • Primary Citation of Related Structures:  
    5E7B, 5E7F, 5E7T

  • PubMed Abstract: 
  • The Gram-positive bacterium Lactococcus lactis, used for the production of cheeses and other fermented dairy products, falls victim frequently to fortuitous infection by tailed phages. The accompanying risk of dairy fermentation failures in industrial facilities has prompted in-depth investigations of these phages ...

    The Gram-positive bacterium Lactococcus lactis, used for the production of cheeses and other fermented dairy products, falls victim frequently to fortuitous infection by tailed phages. The accompanying risk of dairy fermentation failures in industrial facilities has prompted in-depth investigations of these phages. Lactococcal phage Tuc2009 possesses extensive genomic homology to phage TP901-1. However, striking differences in the baseplate-encoding genes stimulated our interest in solving the structure of this host's adhesion device. We report here the X-ray structures of phage Tuc2009 receptor binding protein (RBP) and of a "tripod" assembly of three baseplate components, BppU, BppA, and BppL (the RBP). These structures made it possible to generate a realistic atomic model of the complete Tuc2009 baseplate that consists of an 84-protein complex: 18 BppU, 12 BppA, and 54 BppL proteins. The RBP head domain possesses a different fold than those of phages p2, TP901-1, and 1358, while the so-called "stem" and "neck" domains share structural features with their equivalents in phage TP901-1. The BppA module interacts strongly with the BppU N-terminal domain. Unlike other characterized lactococcal phages, Tuc2009 baseplate harbors two different carbohydrate recognition sites: one in the bona fide RBP head domain and the other in BppA. These findings represent a major step forward in deciphering the molecular mechanism by which Tuc2009 recognizes its saccharidic receptor(s) on its host.


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Marseille, France Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Marseille, France d.vansinderen@ucc.ie cambillau@afmb.univ-mrs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
nanobody L06A, B, C131Camelus dromedariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Major structural protein 1D [auth G],
E [auth H],
F [auth I]
174Lactococcus phage Tuc2009Mutation(s): 0 
UniProt
Find proteins for Q38610 (Lactococcus phage Tuc2009)
Explore Q38610 
Go to UniProtKB:  Q38610
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38610
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.73α = 90
b = 88.04β = 90
c = 147.65γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOLREPphasing
XSCALEdata scaling
XDSdata reduction
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2016-05-04
    Changes: Database references
  • Version 1.3: 2018-10-24
    Changes: Data collection, Source and taxonomy