5V65

Crystal structure of macrocycles containing Abeta 17-23 (LV(PHI)FAED) and Abeta 30-36 (AII(SAR)L(ORN)V)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

X-ray Crystallographic Structure of a Compact Dodecamer from a Peptide Derived from A beta 16-36.

Salveson, P.J., Spencer, R.K., Kreutzer, A.G., Nowick, J.S.

(2017) Org Lett 19: 3462-3465

  • DOI: https://doi.org/10.1021/acs.orglett.7b01445
  • Primary Citation of Related Structures:  
    5V63, 5V64, 5V65

  • PubMed Abstract: 

    The assembly of the β-amyloid peptide, Aβ, into soluble oligomers is associated with neurodegeneration in Alzheimer's disease. The Aβ oligomers are thought to be composed of β-hairpins. Here, the effect of shifting the residue pairing of the β-hairpins on the structures of the oligomers that form is explored through X-ray crystallography. Three residue pairings were investigated using constrained macrocyclic β-hairpins in which Aβ 30-36 is juxtaposed with Aβ 17-23 , Aβ 16-22 , and Aβ 15-21 . The Aβ 16-22 -Aβ 30-36 pairing forms a compact ball-shaped dodecamer composed of fused triangular trimers. This dodecamer may help explain the structures of the trimers and dodecamers formed by full-length Aβ.

    • 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
ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-SAR-LEU-MET-VAL
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
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, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
PHI
Query on PHI
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC9 H10 I N O2PHE
SAR
Query on SAR
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.228 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.719α = 90
b = 67.719β = 90
c = 169.612γ = 120
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: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Advisory, Author supporting evidence, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence, Database references