3EJC | pdb_00003ejc

Full length Receptor Binding Protein from Lactococcal phage TP901-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.238 (Depositor) 
  • R-Value Work: 
    0.192 (Depositor) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure and molecular assignment of lactococcal phage TP901-1 baseplate.

Bebeacua, C.Bron, P.Lai, L.Vegge, C.S.Brondsted, L.Spinelli, S.Campanacci, V.Veesler, D.van Heel, M.Cambillau, C.

(2010) J Biological Chem 285: 39079-39086

  • DOI: https://doi.org/10.1074/jbc.M110.175646
  • Primary Citation Related Structures: 
    3EJC

  • PubMed Abstract: 

    P335 lactococcal phages infect the gram(+) bacterium Lactococcus lactis using a large multiprotein complex located at the distal part of the tail and termed baseplate (BP). The BP harbors the receptor-binding proteins (RBPs), which allow the specific recognition of saccharidic receptors localized on the host cell surface. We report here the electron microscopic structure of the phage TP901-1 wild-type BP as well as those of two mutants bppL (-) and bppU(-), lacking BppL (the RBPs) or both peripheral BP components (BppL and BppU), respectively. We also achieved an electron microscopic reconstruction of a partial BP complex, formed by BppU and BppL. This complex exhibits a tripod shape and is composed of nine BppLs and three BppUs. These structures, combined with light-scattering measurements, led us to propose that the TP901-1 BP harbors six tripods at its periphery, located around the central tube formed by ORF46 (Dit) hexamers, at its proximal end, and a ORF47 (Tal) trimer at its distal extremity. A total of 54 BppLs (18 RBPs) are thus available to mediate host anchoring with a large apparent avidity. TP901-1 BP exhibits an infection-ready conformation and differs strikingly from the lactococcal phage p2 BP, bearing only 6 RBPs, and which needs a conformational change to reach its activated state. The comparison of several Siphoviridae structures uncovers a close organization of their central BP core whereas striking differences occur at the periphery, leading to diverse mechanisms of host recognition.


  • Organizational Affiliation
    • Department of Biological Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 17.99 kDa 
  • Atom Count: 1,342 
  • Modeled Residue Count: 163 
  • Deposited Residue Count: 169 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Baseplate protein (BPP)169Lactococcus phage TP901-1Mutation(s): 0 
Gene Names: bpp
UniProt
Find proteins for Q9G096 (Lactococcus phage TP901-1)
Explore Q9G096 
Go to UniProtKB:  Q9G096
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9G096
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.238 (Depositor) 
  • R-Value Work:  0.192 (Depositor) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.71α = 90
b = 41.71β = 90
c = 465.25γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Refinement description