2OJZ

Anti-DNA antibody ED10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Specific recognition of a DNA immunogen by its elicited antibody

Sanguineti, S.Centeno Crowley, J.M.Lodeiro Merlo, M.F.Cerutti, M.L.Wilson, I.A.Goldbaum, F.A.Stanfield, R.L.de Prat-Gay, G.

(2007) J.Mol.Biol. 370: 183-195

  • DOI: 10.1016/j.jmb.2007.04.046
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA recognition by antibodies is a key feature of autoimmune diseases, yet model systems with structural information are very limited. The monoclonal antibody ED-10 recognizes one of the strands of the DNA duplex used in the immunogenic complex. Modi ...

    DNA recognition by antibodies is a key feature of autoimmune diseases, yet model systems with structural information are very limited. The monoclonal antibody ED-10 recognizes one of the strands of the DNA duplex used in the immunogenic complex. Modifications of the 5' end decrease the binding affinity and short oligonucleotides retain high binding affinity. We determined crystal structures for the Fab bound to a 6-mer oligonucleotide containing the specific sequence that raised the antibody and compared it with the unliganded Fab. Only the first two bases from the 5' end (dTdC) display electron density and we observe four key hydrogen bonds at the interface. The thymine ring is stacked between TrpH50 and TrpH95, and the cytosine ring is packed against TyrL32. Upon DNA binding, TyrH97 and TrpH95 rearrange to allow subnanomolar binding affinity, five orders of magnitude higher than other reported complexes, possibly because of having gone through affinity maturation. This structure represents the first bona fide antibody DNA immunogen complex described in atomic detail.


    Organizational Affiliation

    Instituto Leloir and CONICET, Patricias Argentinas 435, 1405 Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab ED10 light chain
L, M
219Mus musculusMutation(s): 0 
Gene Names: Igkc (Igk-C)
Find proteins for A2NHM3 (Mus musculus)
Go to UniProtKB:  A2NHM3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab ED10 heavy chain
H, I
216Mus spMutation(s): 0 
Gene Names: Mc5 VHCH1
Find proteins for A0N7J2 (Mus sp)
Go to UniProtKB:  A0N7J2
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.899α = 90.00
b = 194.045β = 90.00
c = 61.174γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance