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 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


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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 U S A 103: 6160-6165

  • DOI: https://doi.org/10.1073/pnas.0600865103
  • Primary Citation of Related Structures:  
    2DDQ

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
R310 antibody heavy chainA [auth H]213Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9JL75 (Mus musculus)
Explore Q9JL75 
Go to UniProtKB:  Q9JL75
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JL75
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
R310 antibody light chainB [auth L]218Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HRB
Query on HRB

Download Ideal Coordinates CCD File 
D [auth L]N-ACETYL-1-[(2R,3S,5R)-5-HYDROXY-2-PENTYLTETRAHYDROFURAN-3-YL]-L-HISTIDINE
C17 H27 N3 O5
INPAKWNFLOQYEI-CAOSSQGBSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
C [auth H]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.318α = 90
b = 65.794β = 118.77
c = 64.31γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary