6WXM

X-ray crystallographic structure of a beta-hairpin peptide derived from amyloid beta 16-36

  • Classification: DE NOVO PROTEIN
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-05-11 Released: 2020-07-08 
  • Deposition Author(s): Kreutzer, A.G., 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: 2.30 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray Crystallography Reveals Parallel and Antiparallel beta-Sheet Dimers of a beta-Hairpin Derived from A beta16-36that Assemble to Form Different Tetramers.

Kreutzer, A.G.Samdin, T.D.Guaglianone, G.Spencer, R.K.Nowick, J.S.

(2020) ACS Chem Neurosci 11: 2340-2347

  • DOI: 10.1021/acschemneuro.0c00290
  • Primary Citation of Related Structures:  
    6WXM

  • PubMed Abstract: 
  • High-resolution structures of oligomers formed by the β-amyloid peptide, Aβ, are important for understanding the molecular basis of Alzheimer's disease. Dimers of Aβ are linked to the pathogenesis and progression of Alzheimer's disease, and tetramers of Aβ are neurotoxic ...

    High-resolution structures of oligomers formed by the β-amyloid peptide, Aβ, are important for understanding the molecular basis of Alzheimer's disease. Dimers of Aβ are linked to the pathogenesis and progression of Alzheimer's disease, and tetramers of Aβ are neurotoxic. This paper reports the X-ray crystallographic structures of dimers and tetramers, as well as an octamer, formed by a peptide derived from the central and C -terminal regions of Aβ. In the crystal lattice, the peptide assembles to form two different dimers-an antiparallel β-sheet dimer and a parallel β-sheet dimer-that each further self-assemble to form two different tetramers-a sandwich-like tetramer and a twisted β-sheet tetramer. The structures of these dimers and tetramers derived from Aβ serve as potential models for dimers and tetramers of full-length Aβ that form in vitro and in Alzheimer's disease-afflicted brains.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA.



Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Amyloid-beta protein22Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05067
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ORN
Query on ORN
A [auth F],
B [auth H],
C [auth B],
D [auth I],
E,
A [auth F],
B [auth H],
C [auth B],
D [auth I],
E,
F [auth A],
G [auth C],
H [auth D],
I [auth J],
J [auth G],
K
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
PHI
Query on PHI
A [auth F],
B [auth H],
C [auth B],
D [auth I],
E,
A [auth F],
B [auth H],
C [auth B],
D [auth I],
E,
F [auth A],
G [auth C],
H [auth D],
I [auth J],
J [auth G],
K
L-PEPTIDE LINKINGC9 H10 I N O2PHE
SAR
Query on SAR
A [auth F],
B [auth H],
C [auth B],
D [auth I],
E,
A [auth F],
B [auth H],
C [auth B],
D [auth I],
E,
F [auth A],
G [auth C],
H [auth D],
I [auth J],
J [auth G],
K
PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.194α = 90
b = 122.127β = 90
c = 58.327γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata 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: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Derived calculations
  • Version 1.2: 2020-08-26
    Changes: Database references, Derived calculations