1P2C

crystal structure analysis of an anti-lysozyme antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural mechanism for affinity maturation of an anti-lysozyme antibody.

Cauerhff, A.Goldbaum, F.A.Braden, B.C.

(2004) Proc.Natl.Acad.Sci.USA 101: 3539-3544

  • DOI: 10.1073/pnas.0400060101
  • Also Cited By: 2Q76

  • PubMed Abstract: 
  • In the immune response against a typical T cell-dependent protein antigen, the affinity maturation process is fast and is associated with the early class switch from IgM to IgG. As such, a comprehension of the molecular basis of affinity maturation c ...

    In the immune response against a typical T cell-dependent protein antigen, the affinity maturation process is fast and is associated with the early class switch from IgM to IgG. As such, a comprehension of the molecular basis of affinity maturation could be of great importance in biomedical and biotechnological applications. Affinity maturation of anti-protein antibodies has been reported to be the result of small structural changes, mostly confined to the periphery of the antigen-combining site. However, little is understood about how these small structural changes account for the increase in the affinity toward the antigen. Herein, we present the three-dimensional structure of the Fab fragment from BALB/c mouse mAb F10.6.6 in complex with the antigen lysozyme. This antibody was obtained from a long-term exposure to the antigen. mAb F10.6.6, and the previously described antibody D44.1, are the result of identical or nearly identical somatic recombination events. However, different mutations in the framework and variable regions result in an approximately 10(3) higher affinity for the F10.6.6 antibody. The comparison of the three-dimensional structures of these Fab-lysozyme complexes reveals that the affinity maturation produces a fine tuning of the complementarity of the antigen-combining site toward the epitope, explaining at the molecular level how the immune system is able to increase the affinity of an anti-protein antibody to subnanomolar levels.


    Related Citations: 
    • Lack of significant differences in association rates and affinities of antibodies from short-term and long-term responses to hen egg lysozyme
      Goldbaum, F.A.,Cauerhff, A.,Velikovsky, C.A.,Llera, A.S.,Riottot, M.M.,Poljak, R.J.
      (1999) J.Immunol. 162: 6040


    Organizational Affiliation

    Instituto Leloir, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1405 Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
light chain anti-lysozyme antibody F10.6.6
A, D
212Mus musculusGene Names: Igkc
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
heavy chain VH+CH1 anti-lysozyme antibody F10.6.6
B, E
218Mus musculusGene Names: Ighg1 (Igh-4)
Find proteins for P01868 (Mus musculus)
Go to UniProtKB:  P01868
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
C, F
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.204 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 44.660α = 66.59
b = 73.750β = 74.74
c = 83.780γ = 85.44
Software Package:
Software NamePurpose
CrystalCleardata reduction
CrystalCleardata scaling
CrystalCleardata collection
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance