3A2S

Crystal Structure of outer membrane protein PorB from Neisseria meningitidis in complex with sucrose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB.

Tanabe, M.Nimigean, C.M.Iverson, T.M.

(2010) Proc.Natl.Acad.Sci.USA 107: 6811-6816

  • DOI: 10.1073/pnas.0912115107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PorB is the second most prevalent outer membrane protein in Neisseria meningitidis. PorB is required for neisserial pathogenesis and can elicit a Toll-like receptor mediated host immune response. Here, the x-ray crystal structure of PorB has been det ...

    PorB is the second most prevalent outer membrane protein in Neisseria meningitidis. PorB is required for neisserial pathogenesis and can elicit a Toll-like receptor mediated host immune response. Here, the x-ray crystal structure of PorB has been determined to 2.3 A resolution. Structural analysis and cocrystallization studies identify three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one transports cations nonselectively, and one facilitates the specific uptake of sugars. During infection, PorB likely binds host mitochondrial ATP, and cocrystallization with the ATP analog AMP-PNP suggests that binding of nucleotides regulates these translocation pathways both by partial occlusion of the pore and by restricting the motion of a putative voltage gating loop. PorB is located on the surface of N. meningitidis and can be recognized by receptors of the host innate immune system. Features of PorB suggest that Toll-like receptor mediated recognition outer membrane proteins may be initiated with a nonspecific electrostatic attraction.


    Organizational Affiliation

    Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232-6600, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane protein II
X
355Neisseria meningitidisMutation(s): 0 
Gene Names: porB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
PorB outer membrane protein, native structure
Find proteins for Q5RT80 (Neisseria meningitidis)
Go to UniProtKB:  Q5RT80
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
X
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
LDA
Query on LDA

Download SDF File 
Download CCD File 
X
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.209 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 82.773α = 90.00
b = 82.773β = 90.00
c = 106.433γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance