Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 24.74 kDa 
• Atom Count: 1473 
• Modelled Residue Count: 196 
• Deposited Residue Count: 210 
• Unique protein chains: 1

3NYL

The X-ray structure of an antiparallel dimer of the human amyloid precursor protein E2 domain

• DOI: 10.2210/pdb3NYL/pdb
• Entry: 3NYL supersedes: 1RW6

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-15 Released: 2011-07-13 
• Deposition Author(s): Ha, Y., Hu, J., Lee, S., Liu, X., Wang, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.322 
• R-Value Work: 0.258 
• R-Value Observed: 0.265 

Literature

The X-ray structure of an antiparallel dimer of the human amyloid precursor protein E2 domain.

Wang, Y., Ha, Y.

(2004) Mol Cell 15: 343-353

• PubMed: 15304215 
• DOI: 10.1016/j.molcel.2004.06.037
• Primary Citation of Related Structures:  
  3NYL


• PubMed Abstract: 
  

Amyloid beta-peptide, which forms neuronal and vascular amyloid deposits in Alzheimer's disease, is derived from an integral membrane protein precursor. The biological function of the precursor is currently unclear. Here we describe the X-ray structure of E2, the largest of the three conserved domains of the precursor. The structure of E2 consists of two coiled-coil substructures connected through a continuous helix and bears an unexpected resemblance to the spectrin family of protein structures. E2 can reversibly dimerize in the solution, and the dimerization occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. Heparan sulfate proteoglycans, the putative ligand for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface.

---

Organizational Affiliation: 

Department of Pharmacology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta (A4) protein (Peptidase nexin-II, Alzheimer disease), isoform CRA_b	A	210	Homo sapiens	Mutation(s): 0  Gene Names: APP, hCG_1810805, 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: 2.80 Å
• R-Value Free: 0.322 
• R-Value Work: 0.258 
• R-Value Observed: 0.265 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.589	α = 90
b = 83.589	β = 90
c = 147.341	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SOLVE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-15 
• Released Date: 2011-07-13 
Deposition Author(s): Ha, Y., Hu, J., Lee, S., Liu, X., Wang, Y.
• This entry supersedes: 1RW6

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release