6CL5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.324 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • PubMed Abstract: 
  • The R-type pyocins are high-molecular weight bacteriocins produced by some strains of <i>Pseudomonas aeruginosa </i> to specifically kill other strains of the same species. Structurally, the R-type pyocins are similar to "simple" contractile tails, ...

    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. mm_shn@mail.ru.,Institute of Physics of Biologic Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland. pgleiman@utmb.edu.,Pylum Biosciences, 385 Oyster Point Blvd., Suite 6A, South San Francisco, CA 94080, USA. dean@avidbiotics.com.,Institute of Physics of Biologic Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland. sebuth@utmb.edu.,Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Mikluho Maklaya Str., Moscow 117997, Russia. mm_shn@mail.ru.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tail fiber protein
A, B, C, D, E, F
384Pseudomonas aeruginosaMutation(s): 0 
Gene Names: HR1
Find proteins for Q9KW03 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q9KW03
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.324 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 144.504α = 90.00
b = 155.031β = 90.00
c = 200.481γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
SNSFSwitzerland31003A_127092
EPFL running cost grantSwitzerland577-1

Revision History 

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