Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.98 kDa 
• Atom Count: 3776 
• Modelled Residue Count: 436 
• Deposited Residue Count: 448 
• Unique protein chains: 3

4ONF

Fab fragment of 3D6 in complex with amyloid beta 1-7

• PDB DOI: 10.2210/pdb4ONF/pdb

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


• Deposited: 2014-01-28 Released: 2014-06-11 
• Deposition Author(s): Feinberg, H., Saldanha, J.W., Diep, L., Goel, A., Widom, A., Veldman, G.M., Weis, W.I., Schenk, D., Basi, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Crystal structure reveals conservation of amyloid-beta conformation recognized by 3D6 following humanization to bapineuzumab.

Feinberg, H., Saldanha, J.W., Diep, L., Goel, A., Widom, A., Veldman, G.M., Weis, W.I., Schenk, D., Basi, G.S.

(2014) Alzheimers Res Ther 6: 31-31

• PubMed: 25024748 
• DOI: 10.1186/alzrt261
• Primary Citation of Related Structures:  
  4ONF, 4ONG


• PubMed Abstract: 
  

Immunotherapy targeting amyloid-β peptide is under active clinical investigation for treatment of Alzheimer's disease (AD). Among the hypotheses being investigated for impact on clinical outcome are the preferred epitope or conformation of amyloid-β to target for treatment, and the mechanism of action underlying immunotherapy. Bapineuzumab (humanized 3D6), a neo-epitope specific antibody recognizing amyloid-β1-5 with strong preference for an exposed Asp residue at the N-terminus of the peptide, has undergone advanced clinical testing for treatment of AD.

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Organizational Affiliation: 

Elan Pharmaceuticals, Inc. 300 Technology Sq., Cambridge, MA 02139, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3D6 FAB ANTIBODY HEAVY CHAIN	A [auth H]	222	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3D6 FAB ANTIBODY LIGHT CHAIN	B [auth L]	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	C [auth P]	7	Homo sapiens	Mutation(s): 0  Gene Names: APP, A4, AD1
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.81	α = 90
b = 69.44	β = 115.43
c = 61.73	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
COMO	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-28 
• Released Date: 2014-06-11 
Deposition Author(s): Feinberg, H., Saldanha, J.W., Diep, L., Goel, A., Widom, A., Veldman, G.M., Weis, W.I., Schenk, D., Basi, G.S.

Revision History  

• Version 1.0: 2014-06-11
  Type: Initial release
  
• Version 1.1: 2014-07-30
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description