2X53

Structure of the phage p2 baseplate in its activated conformation with Sr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of Lactococcal Phage P2 Baseplate and its Mechanism of Activation.

Sciara, G.Bebeacua, C.Bron, P.Tremblay, D.Ortiz-Lombardia, M.Lichiere, J.van Heel, M.Campanacci, V.Moineau, S.Cambillau, C.

(2010) Proc Natl Acad Sci U S A 107: 6852

  • DOI: https://doi.org/10.1073/pnas.1000232107
  • Primary Citation of Related Structures:  
    2WZP, 2X53, 4V5I

  • PubMed Abstract: 

    Siphoviridae is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+ Lactococcus lactis possess a baseplate at the tip of their tail involved in host recognition and attachment. Here, we report analysis of the p2 phage baseplate structure by X-ray crystallography and electron microscopy and propose a mechanism for the baseplate activation during attachment to the host cell. This approximately 1 MDa, Escherichia coli-expressed baseplate is composed of three protein species, including six trimers of the receptor-binding protein (RBP). RBPs host-recognition domains point upwards, towards the capsid, in agreement with the electron-microscopy map of the free virion. In the presence of Ca(2+), a cation mandatory for infection, the RBPs rotated 200 degrees downwards, presenting their binding sites to the host, and a channel opens at the bottom of the baseplate for DNA passage. These conformational changes reveal a novel siphophage activation and host-recognition mechanism leading ultimately to DNA ejection.


  • Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098 Centre National de la Recherche Scientifique and Universités d'Aix-Marseille I & II, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF16A [auth 1],
AA [auth Z],
Z [auth Y]
375Lactococcus virus P2Mutation(s): 0 
UniProt
Find proteins for D3KFX5 (Lactococcus phage p2)
Explore D3KFX5 
Go to UniProtKB:  D3KFX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3KFX5
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE RECEPTOR BINDING PROTEIN263Lactococcus virus P2Mutation(s): 0 
UniProt
Find proteins for Q71AW2 (Lactococcus phage p2)
Explore Q71AW2 
Go to UniProtKB:  Q71AW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ71AW2
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ORF15298Lactococcus virus P2Mutation(s): 0 
UniProt
Find proteins for D3WAD3 (Lactococcus phage p2)
Explore D3WAD3 
Go to UniProtKB:  D3WAD3
Entity Groups  
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UniProt GroupD3WAD3
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 300.278α = 90
b = 239.511β = 124.36
c = 274.782γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-12-20
    Changes: Database references, Structure summary
  • Version 1.4: 2019-11-13
    Changes: Data collection, Database references, Other
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description