3VZU

Crystal Structure of outer membrane protein PorB from Neisseria meningitidis in complex with AMP-PNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.0 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
X
355Neisseria meningitidisMutation(s): 0 
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 M4GGR4 (Neisseria meningitidis)
Go to UniProtKB:  M4GGR4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
X
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.237 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 84.482α = 90.00
b = 84.482β = 90.00
c = 106.302γ = 120.00
Software Package:
Software NamePurpose
SHARPphasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release