Biological Assembly 1  

 3D View: Structure | Electron Density

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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: 48981.60 
• Atom Count: 3386 
• Residue Count: 448 
• Unique protein chains: 3

4ONF

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

• DOI: 10.2210/pdb4ONF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus


• 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 Å
• R-Value Free: 0.203 
• R-Value Work: 0.158 

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:  
  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: 

Departments of Structural Biology and of Molecular & Cellular Physiology, 299 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305, USA.,Elan Pharmaceuticals, Inc. 300 Technology Sq., Cambridge, MA 02139, USA.,Pfizer, Cambridge, MA, USA.,Prothena Biosciences, Inc., 650 Gateway Blvd., San Francisco, CA 94080, USA.,Abbvie Bioresearch Center, Worcester, MA, USA.,National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
3D6 FAB ANTIBODY HEAVY CHAIN	H	222	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
3D6 FAB ANTIBODY LIGHT CHAIN	L	219	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Amyloid beta A4 protein	P	7	Homo sapiens	Mutation(s): 0  Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens) Go to Gene View: APP Go to UniProtKB:  P05067

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 126.810	α = 90.00
b = 69.440	β = 115.43
c = 61.730	γ = 90.00

Software Package:

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

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
  Type: Database references
• Version 1.2: 2017-11-22
  Type: Refinement description