2Q76

Mouse anti-hen egg white lysozyme antibody F10.6.6 Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Affinity maturation increases the stability and plasticity of the Fv domain of anti-protein antibodies.

Acierno, J.P.Braden, B.C.Klinke, S.Goldbaum, F.A.Cauerhff, A.

(2007) J.Mol.Biol. 374: 130-146

  • DOI: 10.1016/j.jmb.2007.09.005

  • PubMed Abstract: 
  • The somatic mutations accumulated in variable and framework regions of antibodies produce structural changes that increase the affinity towards the antigen. This implies conformational and non covalent bonding changes at the paratope, as well as poss ...

    The somatic mutations accumulated in variable and framework regions of antibodies produce structural changes that increase the affinity towards the antigen. This implies conformational and non covalent bonding changes at the paratope, as well as possible quaternary structure changes and rearrangements at the V(H)-V(L) interface. The consequences of the affinity maturation on the stability of the Fv domain were studied in a system composed of two closely related antibodies, F10.6.6 and D44.1, which recognize the same hen egg-white lysozyme (HEL) epitope. The mAb F10.6.6 has an affinity constant 700 times higher than D44.1, due to a higher surface complementarity to HEL. The structure of the free form of the Fab F10.6.6 presented here allows a comparative study of the conformational changes produced upon binding to antigen. By means of structural comparison, kinetics and thermodynamics of binding and stability studies on Fab and Fv fragments of both antibodies, we have determined that the affinity maturation process of anti-protein antibodies affects the shape of the combining site and the secondary structure content of the variable domain, stabilizes the V(H)-V(L) interaction, and consequently produces an increase of the Fv domain stability, improving the binding to antigen.


    Related Citations: 
    • 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


    Organizational Affiliation

    Fundación Instituto Leloir, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (IIBBA-CONICET), Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab F10.6.6 fragment Light Chain
A, C
212Mus musculusMutation(s): 0 
Gene Names: Igkc
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab F10.6.6 fragment Heavy Chain
B, D
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.760α = 90.00
b = 80.250β = 91.50
c = 91.500γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance