6CL5

Structure of P. aeruginosa R1 pyocin fiber PALES_06171 comprising C-terminal residues 323-701

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Literature

Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers.

Buth, S.A., Shneider, M.M., Scholl, D., Leiman, P.G.

(2018) Viruses 10

  • DOI: 10.3390/v10080427
  • Primary Citation of Related Structures:  
    6CL5, 6CL6

  • PubMed Abstract: 

    • The R-type pyocins are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. Structurally, the R-type pyocins are similar to "simple" contractile tails, such as those of phage P2 and Mu ...

    The R-type pyocins are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. Structurally, the R-type pyocins are similar to "simple" contractile tails, such as those of phage P2 and Mu. The pyocin recognizes and binds to its target with the help of fibers that emanate from the baseplate structure at one end of the particle. Subsequently, the pyocin contracts its sheath and drives the rigid tube through the host cell envelope. This causes depolarization of the cytoplasmic membrane and cell death. The host cell surface-binding fiber is ~340 Å-long and is attached to the baseplate with its N-terminal domain. Here, we report the crystal structures of C-terminal fragments of the R1 and R2 pyocin fibers that comprise the distal, receptor-binding part of the protein. Both proteins are ~240 Å-long homotrimers in which slender rod-like domains are interspersed with more globular domains-two tandem knob domains in the N-terminal part of the fragment and a lectin-like domain at its C-terminus. The putative substrate binding sites are separated by about 100 Å, suggesting that binding of the fiber to the cell surface causes the fiber to adopt a certain orientation relative to the baseplate and this then triggers sheath contraction.

    Organizational Affiliation: 

    Institute of Physics of Biologic Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland. pgleiman@utmb.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tail fiber protein
A, B, C, D, E, F
A, B, C, D, E, F
384Pseudomonas aeruginosa LESB58Mutation(s): 0 
Gene Names: HR1, CRX60_29890
UniProt
Find proteins for Q9KW03 (Pseudomonas aeruginosa)
Explore Q9KW03 
Go to UniProtKB:  Q9KW03
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KW03
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.504α = 90
b = 155.031β = 90
c = 200.481γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
SNSFSwitzerland31003A_127092
EPFL running cost grantSwitzerland577-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references