1RUP

Crystal structure (G) of native cationic cyclization antibody 4C6 fab at pH 8.5 with a data set collected at APS beamline 19-ID

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.161 

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This is version 1.3 of the entry. See complete history. 


Literature

Probing the antibody-catalyzed water-oxidation pathway at atomic resolution.

Zhu, X., Wentworth Jr., P., Wentworth, A.D., Eschenmoser, A., Lerner, R.A., Wilson, I.A.

(2004) Proc Natl Acad Sci U S A 110: 2247-2252

  • DOI: 10.1073/pnas.0307311101
  • Primary Citation of Related Structures:  
    1RUK, 1RUR, 1RUQ, 1RUP, 1RUM, 1RUL, 1RU9, 1RUA

  • PubMed Abstract: 

    • Antibodies can catalyze the generation of hydrogen peroxide (H2O2) from singlet dioxygen (1O2*) and water via the postulated intermediacy of dihydrogen trioxide (H2O3) and other trioxygen species. Nine different crystal structures were determined to elucidate the chemical consequences to the antibody molecule itself of exposure to such reactive intermediates and to provide insights into the location on the antibody where these species could be generated ...

    Antibodies can catalyze the generation of hydrogen peroxide (H2O2) from singlet dioxygen (1O2*) and water via the postulated intermediacy of dihydrogen trioxide (H2O3) and other trioxygen species. Nine different crystal structures were determined to elucidate the chemical consequences to the antibody molecule itself of exposure to such reactive intermediates and to provide insights into the location on the antibody where these species could be generated. Herein, we report structural evidence for modifications of two specific antibody residues within the interfacial region of the variable and constant domains of different murine antibody antigen-binding fragments (Fabs) by reactive species generated during the antibody-catalyzed water oxidation process. Crystal structure analyses of murine Fabs 4C6 and 13G5 after UV-irradiation revealed complex oxidative modifications to tryptophan L163 and, in 4C6, hydroxylation of the Cgamma of glutamine H6. These discrete modifications of specific residues add further support for the "active site" of the water-oxidation pathway being located within the interfacial region of the constant and variable domains and highlight the general resistance of the antibody molecule to oxidation by reactive oxygen species generated during the water-oxidation process.

    Related Citations: 
    • Structural basis for antibody catalysis of a cationic cyclization reaction
      Zhu, X., Heine, A., Monnat, F., Houk, K.N., Janda, K.D., Wilson, I.A.
      (2003) J Mol Biol 329: 69
    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
immunoglobulin igg2a, heavy chain L219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
immunoglobulin igg2a, light chain H222Mus musculusMutation(s): 0 
Gene Names: Igh-1a
Find proteins for P01865 (Mus musculus)
Explore P01865 
Go to UniProtKB:  P01865
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.161 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.197α = 90
b = 64.197β = 90
c = 266.475γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description