1JFQ

ANTIGEN-BINDING FRAGMENT OF THE MURINE ANTI-PHENYLARSONATE ANTIBODY 36-71, "FAB 36-71"


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural analysis of mutants of high-affinity and low-affinity p-azophenylarsonate-specific antibodies generated by alanine scanning of heavy chain complementarity-determining region 2.

Parhami-Seren, B.Viswanathan, M.Strong, R.K.Margolies, M.N.

(2001) J.Immunol. 167: 5129-5135

  • DOI: 10.4049/jimmunol.167.9.5129

  • PubMed Abstract: 
  • Alanine scanning was used to determine the affinity contributions of 10 side chain amino acids (residues at position 50-60 inclusive) of H chain complementarity-determining region 2 (HCDR2) of the somatically mutated high-affinity anti-p-azophenylars ...

    Alanine scanning was used to determine the affinity contributions of 10 side chain amino acids (residues at position 50-60 inclusive) of H chain complementarity-determining region 2 (HCDR2) of the somatically mutated high-affinity anti-p-azophenylarsonate Ab, 36-71. Each mutated H chain gene was expressed in the context of mutated (36-71L) and the unmutated (36-65L) L chains to also assess the contribution of L chain mutations to affinity. Combined data from fluorescence quenching, direct binding, inhibition, and capture assays indicated that mutating H:Tyr(50) and H:Tyr(57) to Ala in the 36-71 H chain results in significant loss of binding with both mutated (36-71L) or unmutated (36-65L) L chain, although the decrease was more pronounced when unmutated L chain was used. All other HCDR2 mutations in 36-71 had minimal effect on Ab affinity when expressed with 36-71 L chain. However, in the context of unmutated L chain, of H:Gly(54) to Ala resulted in significant loss of binding, while Abs containing Asn(52) to Ala, Pro(53) to Ala, or Ile(58) to Ala mutation exhibited 4.3- to 7.1-fold reduced affinities. When alanine scanning was performed instead on certain HCDR2 residues of the germline-encoded (unmutated) 36-65 Ab and expressed with unmutated L chain as Fab in bacteria, these mutants exhibited affinities similar to or slightly higher than the wild-type 36-65. These findings indicate an important role of certain HCDR2 side chain residues on Ab affinity and the constraints imposed by L chain mutations in maintaining Ag binding.


    Organizational Affiliation

    Department of Biochemistry, College of Medicine, University of Vermont, Burlington, VT 05405, USA. bparhami@zoo.uvm.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIGEN-BINDING FRAGMENT OF ANTI-PHENYLARSONATE ANTIBODY
L
215Mus musculusMutation(s): 0 
Find proteins for P01648 (Mus musculus)
Go to UniProtKB:  P01648
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIGEN-BINDING FRAGMENT OF ANTI-PHENYLARSONATE ANTIBODY
H
222Mus musculusMutation(s): 0 
Find proteins for P01747 (Mus musculus)
Go to UniProtKB:  P01747
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.130α = 90.00
b = 73.050β = 104.48
c = 46.780γ = 90.00
Software Package:
Software NamePurpose
UCSD-systemdata scaling
X-PLORrefinement
X-PLORmodel building
UCSD-systemdata reduction
X-PLORphasing
UCSD-systemdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description