6O3N

Cross-alpha Amyloid-like Structure alphaAmA

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

  • Deposited: 2019-02-26 Released: 2019-03-13 
  • 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

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.299 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

  • 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 asse ...

    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

    Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, CA, USA. william.degrado@ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cross-alpha Amyloid-like Structure alphaAmAABCDEFGHIJKLMNOP27synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.299 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.816α = 90
b = 164.816β = 90
c = 164.134γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata 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 StatesR35GM122603
National Science Foundation (NSF, United States)United StatesCHE1413295

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence