8EC9

Covalently stabilized triangular trimer derived from Abeta16-36 with p-iodo-phenylalanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.277 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Probing differences among A beta oligomers with two triangular trimers derived from A beta.

Kreutzer, A.G.Guaglianone, G.Yoo, S.Parrocha, C.M.T.Ruttenberg, S.M.Malonis, R.J.Tong, K.Lin, Y.F.Nguyen, J.T.Howitz, W.J.Diab, M.N.Hamza, I.L.Lai, J.R.Wysocki, V.H.Nowick, J.S.

(2023) Proc Natl Acad Sci U S A 120: e2219216120-e2219216120

  • DOI: https://doi.org/10.1073/pnas.2219216120
  • Primary Citation of Related Structures:  
    8EC9, 8ECA

  • PubMed Abstract: 

    The assembly of the β-amyloid peptide (Aβ) to form oligomers and fibrils is closely associated with the pathogenesis and progression of Alzheimer's disease. Aβ is a shape-shifting peptide capable of adopting many conformations and folds within the multitude of oligomers and fibrils the peptide forms. These properties have precluded detailed structural elucidation and biological characterization of homogeneous, well-defined Aβ oligomers. In this paper, we compare the structural, biophysical, and biological characteristics of two different covalently stabilized isomorphic trimers derived from the central and C -terminal regions Aβ. X-ray crystallography reveals the structures of the trimers and shows that each trimer forms a ball-shaped dodecamer. Solution-phase and cell-based studies demonstrate that the two trimers exhibit markedly different assembly and biological properties. One trimer forms small soluble oligomers that enter cells through endocytosis and activate capase-3/7-mediated apoptosis, while the other trimer forms large insoluble aggregates that accumulate on the outer plasma membrane and elicit cellular toxicity through an apoptosis-independent mechanism. The two trimers also exhibit different effects on the aggregation, toxicity, and cellular interaction of full-length Aβ, with one trimer showing a greater propensity to interact with Aβ than the other. The studies described in this paper indicate that the two trimers share structural, biophysical, and biological characteristics with oligomers of full-length Aβ. The varying structural, assembly, and biological characteristics of the two trimers provide a working model for how different Aβ trimers can assemble and lead to different biological effects, which may help shed light on the differences among Aβ oligomers.


  • Organizational Affiliation

    Department of Chemistry, University of California Irvine, Irvine, CA 92697.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORN-LYS-LEU-VAL-PHI-PHE-ALA-GLU-ORN-CYS-ILE-ILE-SAR-CYS-MET-VAL
A, B, C, D, E
A, B, C, D, E, F
16synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
ORN
Query on ORN
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
PHI
Query on PHI
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC9 H10 I N O2PHE
SAR
Query on SAR
A, B, C, D, E
A, B, C, D, E, F
PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.277 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.06α = 90
b = 43.06β = 90
c = 92.767γ = 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 on Aging (NIH/NIA)United States1RF1AG062296-01
National Institutes of Health/National Institute on Aging (NIH/NIA)United States1RF1AG072587-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references