5W4I

X-ray crystallographic structure of a beta-hairpin peptide mimic derived from Abeta 16-36. Rigaku data set. (ORN)KLV(MEA)FAE(ORN)AIIGLMV.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Hexamer of a Peptide Derived from A beta 16-36.

Kreutzer, A.G.Spencer, R.K.McKnelly, K.J.Yoo, S.Hamza, I.L.Salveson, P.J.Nowick, J.S.

(2017) Biochemistry 56: 6061-6071

  • DOI: https://doi.org/10.1021/acs.biochem.7b00831
  • Primary Citation of Related Structures:  
    5W4H, 5W4I, 5W4J

  • PubMed Abstract: 

    The absence of high-resolution structures of amyloid oligomers constitutes a major gap in our understanding of amyloid diseases. A growing body of evidence indicates that oligomers of the β-amyloid peptide Aβ are especially important in the progression of Alzheimer's disease. In many Aβ oligomers, the Aβ monomer components are thought to adopt a β-hairpin conformation. This paper describes the design and study of a macrocyclic β-hairpin peptide derived from Aβ 16-36 . Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and size exclusion chromatography studies show that the Aβ 16-36 β-hairpin peptide assembles in solution to form hexamers, trimers, and dimers. X-ray crystallography reveals that the peptide assembles to form a hexamer in the crystal state and that the hexamer is composed of dimers and trimers. Lactate dehydrogenase release assays show that the oligomers formed by the Aβ 16-36 β-hairpin peptide are toxic toward neuronally derived SH-SY5Y cells. Replica-exchange molecular dynamics demonstrates that the hexamer can accommodate full-length Aβ. These findings expand our understanding of the structure, solution-phase behavior, and biological activity of Aβ oligomers and may offer insights into the molecular basis of Alzheimer's disease.


  • Organizational Affiliation

    Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A-beta 17_36: ORN-LYS-LEU-VAL-MEA-PHE-ALA-GLU-ORN-ALA-ILE-ILE-GLY-LEU-MET-VAL
A, B, C
16Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA
A, B, C
L-PEPTIDE LINKINGC10 H13 N O2PHE
ORN
Query on ORN
A, B, C
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.746α = 90
b = 67.746β = 90
c = 67.746γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-11-29
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence