Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Macromolecule Content

• Total Structure Weight: 49.22 kDa 
• Atom Count: 3481 
• Residue Count: 443 
• Unique protein chains: 3

2R0W

PFA2 FAB complexed with Abeta1-8

• DOI: 10.2210/pdb2R0W/pdb

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


• Deposited: 2007-08-21 Released: 2007-10-16 
• Deposition Author(s): Gardberg, A.S., Dealwis, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.277 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

Molecular basis for passive immunotherapy of Alzheimer's disease

Gardberg, A.S., Dice, L.T., Ou, S., Rich, R.L., Helmbrecht, E., Ko, J., Wetzel, R., Myszka, D.G., Patterson, P.H., Dealwis, C.

(2007) Proc Natl Acad Sci U S A 104: 15659-15664

• PubMed: 17895381 
• DOI: 10.1073/pnas.0705888104
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Amyloid aggregates of the amyloid-beta (Abeta) peptide are implicated in the pathology of Alzheimer's disease. Anti-Abeta monoclonal antibodies (mAbs) have been shown to reduce amyloid plaques in vitro and in animal studies. Consequently, passive immunization is being considered for treating Alzheimer's, and anti-Abeta mAbs are now in phase II trials. We report the isolation of two mAbs (PFA1 and PFA2) that recognize Abeta monomers, protofibrils, and fibrils and the structures of their antigen binding fragments (Fabs) in complex with the Abeta(1-8) peptide DAEFRHDS. The immunodominant EFRHD sequence forms salt bridges, hydrogen bonds, and hydrophobic contacts, including interactions with a striking WWDDD motif of the antigen binding fragments. We also show that a similar sequence (AKFRHD) derived from the human protein GRIP1 is able to cross-react with both PFA1 and PFA2 and, when cocrystallized with PFA1, binds in an identical conformation to Abeta(1-8). Because such cross-reactivity has implications for potential side effects of immunotherapy, our structures provide a template for designing derivative mAbs that target Abeta with improved specificity and higher affinity.

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Organizational Affiliation: 

Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
IgG2a Fab fragment light chain	L	219	Mus musculus	Mutation(s): 1  Gene Names: Igkc, Igk-C
Find proteins for A2NHM3 (Mus musculus) Explore A2NHM3  Go to UniProtKB:  A2NHM3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
IgG2a Fab fragment heavy chain, Fd portion	H	223	Mus musculus	Mutation(s): 0
Find proteins for Q811U5 (Mus musculus) Explore Q811U5  Go to UniProtKB:  Q811U5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Amyloid beta peptide fragment	Q	8	N/A	Mutation(s): 0
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
NIH Common Fund Data Resources
PHAROS  P05067

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	L	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	L	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.277 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.793	α = 92.51
b = 43.327	β = 94.96
c = 58.456	γ = 90.55

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-21 
• Released Date: 2007-10-16 
Deposition Author(s): Gardberg, A.S., Dealwis, C.

Revision History 

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description