5GKR

Crystal structure of SLE patient-derived anti-DNA antibody in complex with oligonucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus

Sakakibara, S.Arimori, T.Yamashita, K.Jinzai, H.Motooka, D.Nakamura, S.Li, S.Takeda, K.Katayama, J.El Hussien, M.A.Narazaki, M.Tanaka, T.Standley, D.M.Takagi, J.Kikutani, H.

(2017) Sci Rep 7: 16428-16428

  • DOI: 10.1038/s41598-017-16681-y
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The evolutional process of disease-associated autoantibodies in systemic lupus erythematosus (SLE) remains to be established. Here we show intraclonal diversification and affinity maturation of anti-nuclear antibody (ANA)-producing B cells in SLE. We ...

    The evolutional process of disease-associated autoantibodies in systemic lupus erythematosus (SLE) remains to be established. Here we show intraclonal diversification and affinity maturation of anti-nuclear antibody (ANA)-producing B cells in SLE. We identified a panel of monoclonal ANAs recognizing nuclear antigens, such as double-stranded DNA (dsDNA) and ribonucleoproteins (RNPs) from acute SLE subjects. These ANAs had relatively few, but nonetheless critical mutations. High-throughput immunoglobulin sequencing of blood lymphocytes disclosed the existence of sizable ANA lineages shearing critical mutations intraclonally. We further focused on anti-DNA antibodies, which are capable to bind to both single-stranded (ss) and dsDNA at high affinity. Crystal structure and biochemical analysis confirmed a direct role of the mutations in the acquisition of DNA reactivity and also revealed that these anti-DNA antibodies recognized an unpaired region within DNA duplex. Our study unveils the unique properties of high-affinity anti-DNA antibodies that are generated through antigen-driven affinity maturation in acute phase of SLE.


    Organizational Affiliation

    Laboratory of Immune Regulation, Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan. kikutani@biken.osaka-u.ac.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IgG2, Fab (heavy chain)A, C218Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
lambda, Fab (light chain)B, D216Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*TP*T)-3')T4Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.515α = 90
b = 147.515β = 90
c = 112.807γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references