5SUT | pdb_00005sut

X-ray crystallographic structure of a covalent trimer derived from A-beta 17_36. Synchrotron data set. (ORN)CVFFCED(ORN)AII(SAR)L(ORN)V.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.226 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5SUT

This is version 1.4 of the entry. See complete history

Literature

Stabilization, Assembly, and Toxicity of Trimers Derived from A beta.

Kreutzer, A.G.Yoo, S.Spencer, R.K.Nowick, J.S.

(2017) J Am Chem Soc 139: 966-975

  • DOI: https://doi.org/10.1021/jacs.6b11748
  • Primary Citation Related Structures: 
    5SUR, 5SUS, 5SUT, 5SUU

  • PubMed Abstract: 

    Oligomers of the β-amyloid peptide Aβ have emerged as important contributors to neurodegeneration in Alzheimer's disease. Mounting evidence suggests that Aβ trimers and higher-order oligomers derived from trimers have special significance in the early stages of Alzheimer's disease. Elucidating the structures of these trimers and higher-order oligomers is paramount for understanding their role in neurodegeneration. This paper describes the design, synthesis, X-ray crystallographic structures, and biophysical and biological properties of two stabilized trimers derived from the central and C-terminal regions of Aβ. These triangular trimers are stabilized through three disulfide cross-links between the monomer subunits. The X-ray crystallographic structures reveal that the stabilized trimers assemble hierarchically to form hexamers, dodecamers, and annular porelike structures. Solution-phase biophysical studies reveal that the stabilized trimers assemble in solution to form oligomers that recapitulate some of the higher-order assemblies observed crystallographically. The stabilized trimers share many of the biological characteristics of oligomers of full-length Aβ, including toxicity toward a neuronally derived human cell line, activation of caspase-3 mediated apoptosis, and reactivity with the oligomer-specific antibody A11. These studies support the biological significance of the triangular trimer assembly of Aβ β-hairpins and may offer a deeper understanding of the molecular basis of Alzheimer's disease.


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

Macromolecule Content 

  • Total Structure Weight: 3.61 kDa 
  • Atom Count: 259 
  • Modeled Residue Count: 32 
  • Deposited Residue Count: 32 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
16mer A-beta peptide: ORN-CYS-VAL-PHE-PHE-CYS-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-ORN-VAL
A, B
16Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ORN
Query on ORN
A, B
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
SAR
Query on SAR
A, B
PEPTIDE LINKINGC3 H7 N O2GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.59α = 90
b = 49.59β = 90
c = 64.185γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

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: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Advisory, Author supporting evidence
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-03-27
    Changes: Database references