2DDQ

Crystal Structure of the Fab fragment of a R310 antibody complexed with (R)-HNE-histidine adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bispecific abs against modified protein and DNA with oxidized lipids

Akagawa, M.Ito, S.Toyoda, K.Ishii, Y.Tatsuda, E.Shibata, T.Yamaguchi, S.Kawai, Y.Ishino, K.Kishi, Y.Adachi, T.Tsubata, T.Takasaki, Y.Hattori, N.Matsuda, T.Uchida, K.

(2006) Proc.Natl.Acad.Sci.Usa 103: 6160-6165

  • DOI: 10.1073/pnas.0600865103

  • PubMed Abstract: 
  • 4-Hydroxy-2-nonenal (HNE), a racemic mixture of 4R- and 4S-enantiomers, is a major product of lipid peroxidation and is believed to be largely responsible for the cytopathological effects observed during oxidative stress. HNE reacts with histidine to ...

    4-Hydroxy-2-nonenal (HNE), a racemic mixture of 4R- and 4S-enantiomers, is a major product of lipid peroxidation and is believed to be largely responsible for the cytopathological effects observed during oxidative stress. HNE reacts with histidine to form a stable HNE-histidine Michael addition-type adduct possessing three chiral centers in the cyclic hemiacetal structure. We have previously raised the mAbs, anti-R mAb 310 and anti-S mAb S412, that enantioselectively recognized the R-HNE-histidine and R-HNE-histidine adducts, respectively, and demonstrated the presence of both epitopes in vivo. In the present study, to further investigate the anti-HNE immune response, we analyzed the variable genes and primary structure of these Abs and found that the sequence of R310 was highly homologous to anti-DNA autoantibodies, the hallmark of systemic lupus erythematosus. An x-ray crystallographic analysis of the R310 Fab fragment showed that the R-HNE-histidine adduct binds to a hydrophobic pocket in the antigen-binding site. Despite the structural identity to the anti-DNA autoantibodies, however, R310 showed only a slight crossreactivity with the native double-stranded DNA, whereas the Ab immunoreactivity was dramatically enhanced by the treatment of the DNA with 4-oxo-2-nonenal (ONE), an analog of HNE. Moreover, the 7-(2-oxo-heptyl)-substituted 1,N2-etheno-type ONE-2'-deoxynucleoside adducts were identified as alternative epitopes of R310. Molecular mimicry between the R-HNE-histidine configurational isomers and the ONE-DNA base adducts is proposed for the dual crossreactivity.


    Related Citations: 
    • Crystallization and molecular-replacement studies of the monoclonal antibody mAbR310 specific for the (R)-HNE-modified protein
      Ito, S.,Tatsuda, E.,Ishino, K.,Suzuki, K.,Sakai, H.,Uchida, K.
      (2006) Acta Crystallogr.,Sect.F 62: 562


    Organizational Affiliation

    Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
R310 antibody heavy chain
H
213Mus musculusMutation(s): 0 
Find proteins for Q9JL75 (Mus musculus)
Go to UniProtKB:  Q9JL75
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
R310 antibody light chain
L
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
H
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
HRB
Query on HRB

Download SDF File 
Download CCD File 
L
N-ACETYL-1-[(2R,3S,5R)-5-HYDROXY-2-PENTYLTETRAHYDROFURAN-3-YL]-L-HISTIDINE
C17 H27 N3 O5
INPAKWNFLOQYEI-CAOSSQGBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 127.318α = 90.00
b = 65.794β = 118.77
c = 64.310γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-02-02 
  • Released Date: 2006-07-11 
  • Deposition Author(s): Ito, S.

Revision History 

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance