8T82

Racemic mixture of amyloid beta segment 35-MVGGVV-40 forms heterochiral rippled beta-sheet, includes pentafluoropropionic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Racemic Peptides from Amyloid beta and Amylin Form Rippled beta-Sheets Rather Than Pleated beta-Sheets.

Hazari, A.Sawaya, M.R.Sajimon, M.Vlahakis, N.Rodriguez, J.Eisenberg, D.Raskatov, J.A.

(2023) J Am Chem Soc 145: 25917-25926

  • DOI: https://doi.org/10.1021/jacs.3c11712
  • Primary Citation of Related Structures:  
    8T82, 8T84, 8T86, 8T89

  • PubMed Abstract: 

    The rippled β-sheet was theorized by Pauling and Corey in 1953 as a structural motif in which mirror image peptide strands assemble into hydrogen-bonded periodic arrays with strictly alternating chirality. Structural characterization of the rippled β-sheet was limited to biophysical methods until 2022 when atomic resolution structures of the motif were first obtained. The crystal structural foundation is restricted to four model tripeptides composed exclusively of aromatic residues. Here, we report five new rippled sheet crystal structures derived from amyloid β and amylin, the aggregating toxic peptides of Alzheimer's disease and type II diabetes, respectively. Despite the variation in peptide sequence composition, all five structures form antiparallel rippled β-sheets that extend, like a fibril, along the entire length of the crystalline needle. The long-range packing of the crystals, however, varies. In three of the crystals, the sheets pack face-to-face and exclude water, giving rise to cross-β architectures grossly resembling the steric zipper motif of amyloid fibrils but differing in fundamental details. In the other two crystals, the solvent is encapsulated between the sheets, yielding fibril architectures capable of host-guest chemistry. Our study demonstrates that the formation of rippled β-sheets from aggregating racemic peptide mixtures in three-dimensional (3D) assemblies is a general phenomenon and provides a structural basis for targeting intrinsically disordered proteins.


  • Organizational Affiliation

    Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, California 95064, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
amyloid beta segment 35-MVGGVV-40, racemic mixture6Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
GTEx:  ENSG00000142192 
Entity Groups  
UniProt GroupP05067
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YWK (Subject of Investigation/LOI)
Query on YWK

Download Ideal Coordinates CCD File 
B [auth A]pentafluoropropanoic acid
C3 H F5 O2
LRMSQVBRUNSOJL-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 
  • Space Group: P 1 21/c 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 9.56α = 90
b = 18.57β = 98.4
c = 20.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
SHELXDphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG074954

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Database references