1RUL

Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


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.USA 110: 2247-2252

  • Primary Citation of Related Structures:  1RU9, 1RUA, 1RUK, 1RUM, 1RUP, 1RUQ, 1RUR

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
immunoglobulin igg2a, light chain
L
219N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
immunoglobulin igg2a, heavy chain
H
222Mus musculusGene Names: Igh-1a
Find proteins for P01865 (Mus musculus)
Go to UniProtKB:  P01865
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
L
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
H, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
H
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
4HT
Query on 4HT
L
L-PEPTIDE LINKINGC11 H12 N2 O3TRP
GHG
Query on GHG
H
L-PEPTIDE LINKINGC5 H10 N2 O4GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.206 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.920α = 90.00
b = 63.920β = 90.00
c = 265.725γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXL-97refinement
CNSphasing
HKL-2000data collection
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-02
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2013-06-05
    Type: Non-polymer description