1MPA

BACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bactericidal antibody recognition of a PorA epitope of Neisseria meningitidis: crystal structure of a Fab fragment in complex with a fluorescein-conjugated peptide.

van den Elsen, J.M.Herron, J.N.Hoogerhout, P.Poolman, J.T.Boel, E.Logtenberg, T.Wilting, J.Crommelin, D.J.Kroon, J.Gros, P.

(1997) Proteins 29: 113-125

  • Primary Citation of Related Structures:  2MPA

  • PubMed Abstract: 
  • Class 1 outer membrane protein PorA of Neisseria meningitidis is a vaccine candidate against bacterial meningitis. Antibodies against PorA are able to induce complement-mediated bacterial killing and thereby play an important role in protection again ...

    Class 1 outer membrane protein PorA of Neisseria meningitidis is a vaccine candidate against bacterial meningitis. Antibodies against PorA are able to induce complement-mediated bacterial killing and thereby play an important role in protection against meningococcal disease. Bactericidal antibodies are all directed against variable regions VR1 and VR2 of the PorA sequence, corresponding to loops 1 and 4 of a two-dimensional topology model of the porin with eight extracellular loops. We have determined the crystal structure to 2.6 A resolution of the Fab fragment of bactericidal antibody MN12H2 against meningococcal PorA in complex with a linear fluorescein-conjugated peptide TKDTNNNL derived from the VR2 sequence of sero-subtype P1.7,16 (residues 180-187) from meningococcal strain H44/76. The peptide folds deeply into the binding cavity of the Fab molecule in a type I beta-turn, with the minimal P1.16 epitope DTNNN virtually completely buried. The structure reveals H-bonds and van der Waals interactions with all minimal epitope residues and one essential salt bridge between Asp-182 of the peptide and His-31 of the MN12H2 light chain. The key components of the recognition of PorA epitope P1.16 by bactericidal antibody MN12H2 correspond well with available thermodynamic data from binding studies. Furthermore, they indicate the structural basis of an increased endemic incidence of infection by group B meningococci in England and Wales since 1981 associated with the occurrence of an Neisseria meningitidis escape mutant (strain-MC58). The observed three-dimensional conformation of the peptide provides a rationale for the development of a synthetic peptide vaccine against meningococcal disease.


    Organizational Affiliation

    Department of Pharmaceutics, Faculty of Pharmacy, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MN12H2 IGG2A-KAPPA
L
219Mus musculusGene Names: Igkc (Igk-C)
Find proteins for A2NHM3 (Mus musculus)
Go to UniProtKB:  A2NHM3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MN12H2 IGG2A-KAPPA
H
225Mus musculusGene Names: Ighg
Find proteins for Q569X1 (Mus musculus)
Go to UniProtKB:  Q569X1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PORA P1.16 PEPTIDE FLUORESCEIN CONJUGATE
P
9N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
L
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CYF
Query on CYF
P
L-PEPTIDE LINKINGC25 H23 N3 O7 SCYS
THC
Query on THC
P
L-PEPTIDE LINKINGC6 H11 N O4THR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.680α = 90.00
b = 69.100β = 112.01
c = 72.950γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
X-PLORmodel building
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-04
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance