5V63 | pdb_00005v63

Crystal structure of macrocycles containing Abeta 16-22 (KLV(PHI)FAE) and Abeta 30-36 (AII(SAR)L(ORN)V)

• PDB DOI: https://doi.org/10.2210/pdb5V63/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-03-15 Released: 2017-06-28 
• Deposition Author(s): Spencer, R.K., Salveson, P.J., Nowick, J.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.269 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Literature

X-ray Crystallographic Structure of a Compact Dodecamer from a Peptide Derived from A beta 16-36.

Salveson, P.J., Spencer, R.K., Kreutzer, A.G., Nowick, J.S.

(2017) Org Lett 19: 3462-3465

• PubMed: 28683555 
• DOI: https://doi.org/10.1021/acs.orglett.7b01445
• Primary Citation Related Structures: 
  5V63, 5V64, 5V65


• PubMed Abstract: 
  

  The assembly of the β-amyloid peptide, Aβ, into soluble oligomers is associated with neurodegeneration in Alzheimer's disease. The Aβ oligomers are thought to be composed of β-hairpins. Here, the effect of shifting the residue pairing of the β-hairpins on the structures of the oligomers that form is explored through X-ray crystallography. Three residue pairings were investigated using constrained macrocyclic β-hairpins in which Aβ _30-36 is juxtaposed with Aβ _17-23 , Aβ _16-22 , and Aβ _15-21 . The Aβ _16-22 -Aβ _30-36 pairing forms a compact ball-shaped dodecamer composed of fused triangular trimers. This dodecamer may help explain the structures of the trimers and dodecamers formed by full-length Aβ.

---

Organizational Affiliation: 
• Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 2.02 kDa 
• Atom Count: 140 
• Modeled Residue Count: 16 
• Deposited Residue Count: 17 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORN-LYS-LEU-VAL-PHI-PHE-ALA-GLU-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL	A	17	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ORN	A	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA
PHI	A	L-PEPTIDE LINKING	C9 H10 I N O2		PHE
SAR	A	PEPTIDE LINKING	C3 H7 N O2		GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.269 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.01	α = 90
b = 55.01	β = 90
c = 55.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Spencer, R.K., Salveson, P.J., Nowick, J.S.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM097562

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references
• Version 1.2: 2017-07-26
  Changes: Advisory, Author supporting evidence, Database references
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary