Cross-alpha Amyloid-like Structure alphaAmL, 2nd form

  • Classification: DE NOVO PROTEIN
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2018-04-10 Released: 2019-02-20 
  • Deposition Author(s): Zhang, S.-Q., Liu, L., Degrado, W.F.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Designed peptides that assemble into cross-alpha amyloid-like structures.

Zhang, S.Q.Huang, H.Yang, J.Kratochvil, H.T.Lolicato, M.Liu, Y.Shu, X.Liu, L.DeGrado, W.F.

(2018) Nat Chem Biol 14: 870-875

  • DOI: https://doi.org/10.1038/s41589-018-0105-5
  • Primary Citation of Related Structures:  
    6C4X, 6C4Y, 6C4Z, 6C50, 6C51, 6C52, 6D02, 6O3N

  • PubMed Abstract: 

    Amyloids adopt 'cross-β' structures composed of long, twisted fibrils with β-strands running perpendicular to the fibril axis. Recently, a toxic peptide was proposed to form amyloid-like cross-α structures in solution, with a planar bilayer-like assembly observed in the crystal structure. Here we crystallographically characterize designed peptides that assemble into spiraling cross-α amyloid-like structures, which resemble twisted β-amyloid fibrils. The peptides form helical dimers, stabilized by packing of small and apolar residues, and the dimers further assemble into cross-α amyloid-like fibrils with superhelical pitches ranging from 170 Å to 200 Å. When a small residue that appeared critical for packing was converted to leucine, it resulted in structural rearrangement to a helical polymer. Fluorescently tagged versions of the designed peptides form puncta in mammalian cells, which recover from photobleaching with markedly different kinetics. These structural folds could be potentially useful for directing in vivo protein assemblies with predetermined spacing and stabilities.

  • Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alpha-Amyloid peptide alphaAmL27synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.546α = 90
b = 107.777β = 90
c = 99.374γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

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 StatesR35GM122603
National Science Foundation (NSF, United States)United StatesCHE1413295

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description