1JV5

Anti-blood group A Fv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of an anti-blood group A Fv and improvement of its binding affinity without loss of specificity.

Thomas, R.Patenaude, S.I.MacKenzie, C.R.To, R.Hirama, T.Young, N.M.Evans, S.V.

(2002) J Biol Chem 277: 2059-2064

  • DOI: 10.1074/jbc.M104364200
  • Primary Citation of Related Structures:  
    1JV5

  • PubMed Abstract: 
  • The specificity of antibody recognition of the ABO blood group trisaccharide antigens has been explored by crystal structure analysis and mutation methods. The crystal structure of the Fv corresponding to the anti-blood group A antibody AC1001 has be ...

    The specificity of antibody recognition of the ABO blood group trisaccharide antigens has been explored by crystal structure analysis and mutation methods. The crystal structure of the Fv corresponding to the anti-blood group A antibody AC1001 has been determined to 2.2-A resolution and reveals a binding pocket that is complementary to the blood group A-trisaccharide antigen. The effect of mutating specific residues lining this pocket on binding to the A and B blood group oligosaccharide antigens was investigated through a panel of single point mutations and through a phage library of mutations in complementarity determining region H3. Both approaches gave several mutants with improved affinity for antigen. Surface plasmon resonance indicated up to 8-fold enhancement in affinity for the A-pentasaccharide with no observable binding to the blood group B antigen. This is the first example of single point mutations in a carbohydrate-binding antibody resulting in significant increases in binding affinity without loss of specificity.


    Related Citations: 
    • Production, crystallization and diffraction to atomic resolution of an antibody Fv specific for the blood-group A oligosaccharide antigen
      Patenaude, S.I., MacKenzie, C.R., Bilous, D., To, R.J., Ryan, S.E., Young, N.M., Evans, S.V.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 1456

    Organizational Affiliation

    Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ig kappa chain precursor V regionA107Homo sapiensMutation(s): 0 
Gene Names: IGKV1-33
Find proteins for P01594 (Homo sapiens)
Explore P01594 
Go to UniProtKB:  P01594
NIH Common Fund Data Resources
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ig chain heavy chain precursor V regionB117Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.71α = 90
b = 57.96β = 90
c = 83.58γ = 90
Software Package:
Software NamePurpose
CAD4data collection
ROTAVATAdata reduction
MERLOTphasing
X-PLORrefinement
CAD4data reduction
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-04-18
    Changes: Data collection