Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.41 kDa 
• Atom Count: 4017 
• Modelled Residue Count: 440 
• Deposited Residue Count: 481 
• Unique protein chains: 3

3IFN

X-ray structure of amyloid beta peptide:antibody (Abeta1-40:12A11) complex

• DOI: 10.2210/pdb3IFN/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2009-07-24 Released: 2009-11-17 
• Deposition Author(s): Weis, W.I., Feinberg, H., Basi, G.S., Schenk, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.212 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

Structural correlates of antibodies associated with acute reversal of amyloid beta-related behavioral deficits in a mouse model of Alzheimer disease.

Basi, G.S., Feinberg, H., Oshidari, F., Anderson, J., Barbour, R., Baker, J., Comery, T.A., Diep, L., Gill, D., Johnson-Wood, K., Goel, A., Grantcharova, K., Lee, M., Li, J., Partridge, A., Griswold-Prenner, I., Piot, N., Walker, D., Widom, A., Pangalos, M.N., Seubert, P., Jacobsen, J.S., Schenk, D., Weis, W.I.

(2010) J Biol Chem 285: 3417-3427

• PubMed: 19923222 
• DOI: 10.1074/jbc.M109.045187
• Primary Citation of Related Structures:  
  3IFL, 3IFN, 3IFO, 3IFP


• PubMed Abstract: 
  

Immunotherapy targeting of amyloid beta (Abeta) peptide in transgenic mouse models of Alzheimer disease (AD) has been widely demonstrated to resolve amyloid deposition as well as associated neuronal, glial, and inflammatory pathologies. These successes have provided the basis for ongoing clinical trials of immunotherapy for treatment of AD in humans. Acute as well as chronic Abeta-targeted immunotherapy has also been demonstrated to reverse Abeta-related behavioral deficits assessing memory in AD transgenic mouse models. We observe that three antibodies targeting the same linear epitope of Abeta, Abeta(3-7), differ in their ability to reverse contextual fear deficits in Tg2576 mice in an acute testing paradigm. Reversal of contextual fear deficit by the antibodies does not correlate with in vitro recognition of Abeta in a consistent or correlative manner. To better define differences in antigen recognition at the atomic level, we determined crystal structures of Fab fragments in complex with Abeta. The conformation of the Abeta peptide recognized by all three antibodies was highly related and is also remarkably similar to that observed in independently reported Abeta:antibody crystal structures. Sequence and structural differences between the antibodies, particularly in CDR3 of the heavy chain variable region, are proposed to account for differing in vivo properties of the antibodies under study. These findings provide a structural basis for immunotherapeutic strategies targeting Abeta species postulated to underlie cognitive deficits in AD.

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Organizational Affiliation: 

Elan Pharmaceuticals, Incorporated, South San Francisco, California 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12A11 FAB antibody heavy chain	H	222	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
12A11 FAB antibody light chain	L	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	P	40	Homo sapiens	Mutation(s): 0  Gene Names: APP, A4, AD1
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
NIH Common Fund Data Resources
PHAROS:  P05067

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.212 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.99	α = 90
b = 87.01	β = 95.77
c = 58.99	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-24 
• Released Date: 2009-11-17 
Deposition Author(s): Weis, W.I., Feinberg, H., Basi, G.S., Schenk, D.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-06-19
  Changes: Database references