4Q8D

Crystal structure of a macrocyclic beta-sheet peptide containing two beta-strands from amyloid beta residues 15-23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.746 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Fibril-Like Assembly of Oligomers of a Peptide Derived from beta-Amyloid.

Pham, J.D.Spencer, R.K.Chen, K.H.Nowick, J.S.

(2014) J.Am.Chem.Soc. 136: 12682-12690

  • DOI: 10.1021/ja505713y

  • PubMed Abstract: 
  • A macrocyclic β-sheet peptide containing two nonapeptide segments based on Aβ(15-23) (QKLVFFAED) forms fibril-like assemblies of oligomers in the solid state. The X-ray crystallographic structure of macrocyclic β-sheet peptide 3 was determined at 1.7 ...

    A macrocyclic β-sheet peptide containing two nonapeptide segments based on Aβ(15-23) (QKLVFFAED) forms fibril-like assemblies of oligomers in the solid state. The X-ray crystallographic structure of macrocyclic β-sheet peptide 3 was determined at 1.75 Å resolution. The macrocycle forms hydrogen-bonded dimers, which further assemble along the fibril axis in a fashion resembling a herringbone pattern. The extended β-sheet comprising the dimers is laminated against a second layer of dimers through hydrophobic interactions to form a fibril-like assembly that runs the length of the crystal lattice. The second layer is offset by one monomer subunit, so that the fibril-like assembly is composed of partially overlapping dimers, rather than discrete tetramers. In aqueous solution, macrocyclic β-sheet 3 and homologues 4 and 5 form discrete tetramers, rather than extended fibril-like assemblies. The fibril-like assemblies of oligomers formed in the solid state by macrocyclic β-sheet 3 represent a new mode of supramolecular assembly not previously observed for the amyloidogenic central region of Aβ. The structures observed at atomic resolution for this peptide model system may offer insights into the structures of oligomers and oligomer assemblies formed by full-length Aβ and may provide a window into the propagation and replication of amyloid oligomers.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
macrocyclic beta-sheet peptide incorporating residues amyloid beta 15-23
A, B
18N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ORN
Query on ORN
A, B
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
PHI
Query on PHI
A, B
L-PEPTIDE LINKINGC9 H10 I N O2PHE
HAO
Query on HAO
A, B
peptide-likeC10 H11 N3 O5

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.746 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 32.174α = 90.00
b = 62.852β = 89.98
c = 20.094γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SOLVEphasing
PHENIXrefinement
SCALAdata scaling
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references