3VY8

Crystal Structure of PorB from Neisseria meningitidis in complex with Cesium ion, space group P63

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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This is version 1.1 of the entry. See complete history. 


Literature

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: 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 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Outer membrane proteinA [auth X]355Neisseria meningitidisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CS
Query on CS
Download Ideal Coordinates CCD File 
B [auth X],
C [auth X],
D [auth X]		CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.201α = 90
b = 83.201β = 90
c = 106.415γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
Regidmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
Regidphasing

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