Crystal structure of PorB from Neisseria meningitidis in complex with cesium ion, space group H32

Experimental Data Snapshot

  • Resolution: 2.63 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 

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Identification of a cation transport pathway in Neisseria meningitidis PorB.

Kattner, C.Zaucha, J.Jaenecke, F.Zachariae, U.Tanabe, M.

(2013) Proteins 81: 830-840

  • DOI: https://doi.org/10.1002/prot.24241
  • Primary Citation of Related Structures:  
    3VY8, 3VY9

  • PubMed Abstract: 

    Neisseria meningitidis is the main causative agent of bacterial meningitis. In its outer membrane, the trimeric Neisserial porin PorB is responsible for the diffusive transport of essential hydrophilic solutes across the bilayer. Previous molecular dynamics simulations based on the recent crystal structure of PorB have suggested the presence of distinct solute translocation pathways through this channel. Although PorB has been electrophysiologically characterized as anion-selective, cation translocation through nucleotide-bound PorB during pathogenesis is thought to be instrumental for host cell death. As a result, we were particularly interested in further characterizing cation transport through the pore. We combined a structural approach with additional computational analysis. Here, we present two crystal structures of PorB at 2.1 and 2.65 Å resolution. The new structures display additional electron densities around the protruding loop 3 (L3) inside the pore. We show that these electron densities can be identified as monovalent cations, in our case Cs(+), which are tightly bound to the inner channel. Molecular dynamics simulations reveal further ion interactions and the free energy landscape for ions inside PorB. Our results suggest that the crystallographically identified locations of Cs(+) form a cation transport pathway inside the pore. This finding suggests how positively charged ions are translocated through PorB when the channel is inserted into mitochondrial membranes during Neisserial infection, a process which is considered to dissipate the mitochondrial transmembrane potential gradient and thereby induce apoptosis.

  • Organizational Affiliation

    HALOmem, Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane proteinA [auth X]355Neisseria meningitidisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.63 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.208α = 90
b = 144.208β = 90
c = 106.411γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description