7JXN

Beta hairpin derived from Abeta17-36 with an F20Cha mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.283 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Phenylalanine Mutation to Cyclohexylalanine Facilitates Triangular Trimer Formation by beta-Hairpins Derived from A beta.

Haerianardakani, S.Kreutzer, A.G.Salveson, P.J.Samdin, T.D.Guaglianone, G.E.Nowick, J.S.

(2020) J Am Chem Soc 142: 20708-20716

  • DOI: 10.1021/jacs.0c09281
  • Primary Citation of Related Structures:  
    7JXO, 7JXN

  • PubMed Abstract: 
  • Oligomers of the β-amyloid peptide, Aβ, play a central role in the pathogenesis and progression of Alzheimer's disease. Trimers and higher-order oligomers composed of trimers are thought to be the most neurotoxic Aβ oligomers. To gain insights into the structure and assembly of Aβ oligomers, our laboratory has previously designed and synthesized macrocyclic peptides derived from Aβ 17-23 and Aβ 30-36 that fold to form β-hairpins and assemble to form trimers ...

    Oligomers of the β-amyloid peptide, Aβ, play a central role in the pathogenesis and progression of Alzheimer's disease. Trimers and higher-order oligomers composed of trimers are thought to be the most neurotoxic Aβ oligomers. To gain insights into the structure and assembly of Aβ oligomers, our laboratory has previously designed and synthesized macrocyclic peptides derived from Aβ 17-23 and Aβ 30-36 that fold to form β-hairpins and assemble to form trimers. In this study, we found that mutating Phe 20 to cyclohexylalanine (Cha) in macrocyclic Aβ-derived peptides promotes crystallization of an Aβ-derived peptide containing the Aβ 24-29 loop (peptide 3 F20Cha ) and permits elucidation of its structure and assembly by X-ray crystallography. X-ray crystallography shows that peptide 3 F20Cha forms a hexamer. X-ray crystallography and SDS-PAGE further show that trimer 4 F20Cha , a covalently stabilized trimer derived from peptide 3 F20Cha , forms a dodecamer. Size exclusion chromatography shows that trimer 4 F20Cha forms higher-order assemblies in solution. Trimer 4 F20Cha exhibits cytotoxicity against the neuroblastoma cell line SH-SY5Y. These studies demonstrate the use of the F20Cha mutation to further stabilize oligomers of Aβ-derived peptides that contain more of the native sequence and thus better mimic the oligomers formed by full-length Aβ.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Amyloid-beta 17-36 peptideA, B, C, D21Homo sapiensMutation(s): 0 
Gene Names: APPA4AD1
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], G [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
H7V
Query on H7V
A, B, C, DL-PEPTIDE LINKINGC10 H19 N O2ALA
ORN
Query on ORN
A, B, C, DL-PEPTIDE LINKINGC5 H12 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.283 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.167α = 90
b = 37.167β = 90
c = 116.994γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097562

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references