6VU4 | pdb_00006vu4

Structure of a beta-hairpin peptide mimic derived from Abeta 14-36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Effects of N-Terminal Residues on the Assembly of Constrained beta-Hairpin Peptides Derived from A beta.

Samdin, T.D.Wierzbicki, M.Kreutzer, A.G.Howitz, W.J.Valenzuela, M.Smith, A.Sahrai, V.Truex, N.L.Klun, M.Nowick, J.S.

(2020) J Am Chem Soc 142: 11593-11601

  • DOI: https://doi.org/10.1021/jacs.0c05186
  • Primary Citation of Related Structures:  
    6VU4

  • PubMed Abstract: 

    This paper describes the synthesis, solution-phase biophysical studies, and X-ray crystallographic structures of hexamers formed by macrocyclic β-hairpin peptides derived from the central and C-terminal regions of Aβ, which bear "tails" derived from the N-terminus of Aβ. Soluble oligomers of the β-amyloid peptide, Aβ, are thought to be the synaptotoxic species responsible for neurodegeneration in Alzheimer's disease. Over the last 20 years, evidence has accumulated that implicates the N-terminus of Aβ as a region that may initiate the formation of damaging oligomeric species. We previously studied, in our laboratory, macrocyclic β-hairpin peptides derived from Aβ 16-22 and Aβ 30-36 , capable of forming hexamers that can be observed by X-ray crystallography and SDS-PAGE. To better mimic oligomers of full length Aβ, we use an orthogonal protecting group strategy during the synthesis to append residues from Aβ 1-14 to the parent macrocyclic β-hairpin peptide 1 , which comprises Aβ 16-22 and Aβ 30-36 . The N-terminally extended peptides N+1 , N+2 , N+4 , N+6 , N+8 , N+10 , N+12 , and N+14 assemble to form dimers, trimers, and hexamers in solution-phase studies. X-ray crystallography reveals that peptide N+1 assembles to form a hexamer that is composed of dimers and trimers. These observations are consistent with a model in which the assembly of Aβ oligomers is driven by hydrogen bonding and hydrophobic packing of the residues from the central and C-terminal regions, with the N-terminus of Aβ accommodated by the oligomers as an unstructured tail.


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

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-hairpin Amyloid-beta precursor peptide mimicA [auth C],
B [auth A]
17Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA
A [auth C],
B [auth A]
L-PEPTIDE LINKINGC10 H13 N O2PHE
ORN
Query on ORN
A [auth C],
B [auth A]
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.88α = 90
b = 96.88β = 90
c = 96.88γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata 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: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description