Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 48.53 kDa 
• Atom Count: 3902 
• Modelled Residue Count: 441 
• Deposited Residue Count: 441 
• Unique protein chains: 2

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

• DOI: 10.2210/pdb1RUP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• 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: 1.40 Å
• R-Value Free: 0.212 
• R-Value Work: 0.161 

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

• PubMed: 14982995 
• 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. 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: 

• 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

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin igg2a, heavy chain	A [auth L]	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin igg2a, light chain	B [auth H]	222	Mus musculus	Mutation(s): 0  Gene Names: Igh-1a
UniProt
Find proteins for P01865 (Mus musculus) Explore P01865  Go to UniProtKB:  P01865

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	C [auth H]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
GOL	D [auth H], E [auth H], F [auth H], G [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 64.197	α = 90
b = 64.197	β = 90
c = 266.475	γ = 90

Software Package:

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

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
  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