2BRR

Complex of the neisserial PorA P1.4 epitope peptide and two Fab- fragments (antibody MN20B9.34)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of an Anti-Meningococcal Subtype P1.4 Pora Antibody Provides Basis for Peptide- Vaccine Design.

Oomen, C.J.Hoogerhout, P.Kuipers, B.Vidarsson, G.Van Alphen, L.Gros, P.

(2005) J.Mol.Biol. 351: 1070

  • DOI: 10.1016/j.jmb.2005.06.061

  • PubMed Abstract: 
  • In various western countries, subtype P1.4 of Neisseria meningitidis serogroup B causes the greatest incidence of meningococcal disease. To investigate the molecular recognition of this subtype, we crystallised a peptide (P1HVVVNNKVATH(P11)), corresp ...

    In various western countries, subtype P1.4 of Neisseria meningitidis serogroup B causes the greatest incidence of meningococcal disease. To investigate the molecular recognition of this subtype, we crystallised a peptide (P1HVVVNNKVATH(P11)), corresponding to the subtype P1.4 epitope sequence of outer membrane protein PorA, in complex with a Fab fragment of the bactericidal antibody MN20B9.34 directed against this epitope. Structure determination at 1.95 A resolution revealed a unique complex of one P1.4 antigen peptide bound to two identical Fab fragments. One Fab recognises the putative epitope residues in a 2:2 type I beta-turn at residues P5NNKV(P8), whereas the other Fab binds the C-terminal residues of the peptide that we consider a crystallisation artefact. Interestingly, recognition of the P1.4 epitope peptide is mediated almost exclusively through the complementarity-determining regions of the heavy chain. We exploited the observed turn conformation for designing conformationally restricted cyclic peptides for use as a peptide vaccine. The conformational stability of the two peptide designs was assessed by molecular dynamics simulations. Unlike the linear peptide, both cyclic peptides, conjugated to tetanus toxoid as a carrier protein, elicited antibody responses in mice that recognised meningococci of subtype P1.7-2,4. Serum bactericidal assays showed that some, but not all, of the sera induced with the cyclic peptide conjugates could activate the complement system with titres that were very high compared to the titres induced by complete PorA protein in its native conformation administered in outer membrane vesicles.


    Organizational Affiliation

    Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MN20B9.34 ANTI-P1.4 ANTIBODY, FAB HEAVY CHAIN
H, Y
225N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MN20B9.34 ANTI-P1.4 ANTIBODY, FAB LIGHT CHAIN
L, X
215N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2
P
13Neisseria meningitidisGene Names: porA
Find proteins for Q51183 (Neisseria meningitidis)
Go to UniProtKB:  Q51183
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
X, Y
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
X
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
P
NON-POLYMERH2 N

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ACE
Query on ACE
P
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.666α = 90.00
b = 63.833β = 86.58
c = 124.701γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2012-05-16
    Type: Other