2V7H

Crystal structure of an immunogen specific anti-mannopyranoside monoclonal antibody Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Role of Antibody Paratope Conformational Flexibility in the Manifestation of Molecular Mimicry.

Krishnan, L.Sahni, G.Kaur, K.J.Salunke, D.M.

(2008) Biophys.J. 94: 1367

  • DOI: 10.1529/biophysj.107.108654

  • PubMed Abstract: 
  • Molecular mimicry is a recurrent theme in host defense processes. The correlation of functional mimicry with the structural features of the antibody paratope has been investigated, addressing the consequences of mimicry in host immune mechanisms. Two ...

    Molecular mimicry is a recurrent theme in host defense processes. The correlation of functional mimicry with the structural features of the antibody paratope has been investigated, addressing the consequences of mimicry in host immune mechanisms. Two anti-mannopyranoside antibodies, 1H7 and 2D10, representing the possible extremes of the recognition spectrum with regard to peptide-carbohydrate mimicry were examined. Crystallographic and molecular dynamics simulation analyses established correlation between the antibody flexibility and the manifestation of mimicry. It was evident that monoclonal antibody (mAb) 1H7, which has a narrow specificity in favor of the immunizing antigen, exhibited structural invariance. On the other hand, the antigen-combining site of 2D10, the mimicry-recognizing antibody, showed substantial divergence in the complementarity determining region loops. The docking of mannopyranoside within the antibody paratope revealed multiple modes of binding of the carbohydrate antigen in mAb 2D10 vis à vis single docking mode in mAb 1H7, which overlapped with the common monosaccharide binding site defined in anti-carbohydrate antibodies. The presence of additional antigen binding modes is perhaps reflective of the utilization of conformational flexibility in molecular mimicry. A relatively broader recognition repertoire--attributable to paratope flexibility--may facilitate the recognition of altered antigens of invading pathogens while the antibodies with narrow recognition specificity maintain the fidelity of the response.


    Organizational Affiliation

    National Institute of Immunology, New Delhi, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MONOCLONAL ANTIBODY
A, L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MONOCLONAL ANTIBODY
B, H
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.021α = 90.00
b = 79.737β = 90.75
c = 132.276γ = 90.00
Software Package:
Software NamePurpose
AUTOMARdata scaling
CNSrefinement
AUTOMARdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance