Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47138.07 
• Atom Count: 3310 
• Residue Count: 435 
• Unique protein chains: 2

1RUR

Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set collected at SSRL beamline 9-1.

• DOI: 10.2210/pdb1RUR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus


• Deposited: 2003-12-11 Released: 2004-03-02 
• Deposition Author(s): Zhu, X., Wentworth Jr., P., Wentworth, A.D., Eschenmoser, A., Lerner, R.A., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 

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

• PubMed: 14982995 
• DOI: 10.1073/pnas.0307311101
• Primary Citation of Related Structures:  
  1RUM, 1RUP, 1RUL, 1RUA, 1RUQ, 1RUK, 1RU9


• 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. 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.

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Related Citations: 

• An antibody exo diels-alderase inhibitor complex at 1.95 angstrom resolution
  Heine, A.,Stura, E.A.,Yli-kauhaluoma, J.T.,Gao, C.,Deng, Q.,Beno, B.R.,Houk, K.N.,Janda, K.D.,Wilson, I.A.
  (1998) Science 279: 1934




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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
Molecule	Chains	Sequence Length	Organism	Details
immunoglobulin 13G5, light chain	L	217	Mus musculus	Mutation(s): 0  Gene Names: Igkc
Find proteins for P01837 (Mus musculus) Go to UniProtKB:  P01837

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
immunoglobulin 13G5, heavy chain	H	218	Mus musculus	Mutation(s): 0  Gene Names: Igh
Find proteins for Q569W9 (Mus musculus) Go to UniProtKB:  Q569W9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	L	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 179.275	α = 90.00
b = 40.310	β = 109.91
c = 67.631	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNS	phasing
SHELXL-97	refinement
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-11 
• Released Date: 2004-03-02 
• Deposition Author(s): Zhu, X., Wentworth Jr., P., Wentworth, A.D., Eschenmoser, A., Lerner, R.A., Wilson, I.A.

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: Version format compliance
• Version 1.3: 2019-07-24
  Type: Advisory, Data collection, Refinement description