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Cryo-EM structure of disease-related prion fibrils provides insights into seeding barriers

Nature Structural & Molecular Biology volume 29, pages 962–965 (2022)Cite this article

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Abstract

One of the least understood aspects of prion diseases is the structure of infectious prion protein aggregates. Here we report a high-resolution cryo-EM structure of amyloid fibrils formed by human prion protein with the Y145Stop mutation that is associated with a familial prion disease. This structural insight allows us not only to explain previous biochemical findings, but also provides direct support for the conformational adaptability model of prion transmissibility barriers.

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Fig. 1: Cryo-EM structure of huPrP23-144 amyloid fibrils.
Fig. 2: Solvent-exposed amino acid residues at the top and bottom ends of huPrP23-144 fibrils.

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Data availability

Cryo-EM density map and the atomic models of human PrP23-144 fibrils have been deposited to the Electron Microscopy Data Bank and Protein Data Bank with accession codes EMD-24514 and 7RL4, respectively. Those for mouse PrP23-144 fibrils have been deposited with accession codes EMD-27458 and 8DJA, respectively. Coordinates used in structure comparison are available at the Protein Data Bank with accession codes 6UUR, 7LNA, 6LNI and 7DWV. All main data supporting the findings of this study are available within the article, Extended Data and Supplementary Information.

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Acknowledgements

This work was supported by NIH grants GM094357 (C.P.J. and W.K.S.) and NS103848 (W.K.S.). We thank K. Li for help with acquisition of cryo-EM data. We are grateful to the Cryo-EM Core at CWRU School of Medicine (especially S. Chakrapani and K. Li) for access to cryo-EM instrumentation.

Author information

Authors and Affiliations

  1. Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA

    Qiuye Li & Witold K. Surewicz

  2. Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA

    Christopher P. Jaroniec

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  1. Qiuye Li
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Contributions

Q.L. and W.K.S. designed the study. Q.L. prepared fibrils, collected AFM and EM data, and performed image processing and model building. Q.L., C.P.J. and W.K.S. wrote the manuscript.

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Correspondence to Witold K. Surewicz.

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The authors declare no competing interests.

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Nature Structural & Molecular Biology thanks Byron Caughey and Cong Liu for their contribution to the peer review of this work. Primary Handling Editor: Florian Ullrich, in collaboration with the Nature Structural & Molecular Biology team. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Morphology of huPrP23-144 amyloid fibrils.

a, Cryo-EM image showing the sole morphology with an apparent twist observed for these fibrils, the same fibril morphology was observed in at least 600 images. b, Manually assembled full pitch of huPrP23-144 fibrils from multiple 2D class averages. The entire fibril has a thickness of ~20 nm and the highly ordered amyloid core has a thickness of ~10 nm. c, AFM image of huPrP23-144 fibrils. A representative fibril in the green box is enlarged to show the left-handed twist, the same fibril morphology was observed in at least 20 images.

Extended Data Fig. 2 Fourier shell correlation curves for huPrP23-144 amyloid fibrils.

Fourier shell correlation between two independently refined half-maps is shown in red and Fourier shell correlation between the map and the atomic model is shown in blue.

Extended Data Fig. 3 Non-planar architecture of two representative huPrP23-144 protofilaments assembled through large hydrophobic interfaces.

Subunit n in protofilament A interacts with two subunits in protofilament B (subunits m and m + 1); subunit m + 1 in protofilament B interacts with two subunits in protofilament A (subunits n and n + 1). Such a non-planar conformation results in rugged surfaces at fibril ends, with N-terminal residues at the top end and C-terminal residues at the bottom end exposed to water. A similar non-planar assembly is observed for subunits in protofilaments C and D.

Extended Data Fig. 4 Comparison of the structural model for huPrP23-144 fibrils determined herein by cryo-EM (a) with the low-resolution model previously suggested based on ssNMR data9,12 (b).

Selected residues involved in close interactions between side-chains in these two models are labeled in red (Ala117-Ile139), yellow (Ala115-Leu125), and green (Gly119-Ser135).

Extended Data Fig. 5 Cryo-EM structure of amyloid fibrils generated from moPrP23-144.

a, b, Two types of polymorphs can be found in AFM images (a) and cryo-EM micrographs (b). Polymorph 1 (red arrows) showed a larger left-handed twist like huPrP23-144 fibrils, and polymorph 2 (green arrows) showed a much smaller right-handed twist. The same fibril morphologies were observed in at least 1,000 cryo-EM images or 20 AFM images for each type of sample. c, Manually assembled half-pitch of both polymorphs from multiple 2D class averages. d, 3D maps of moPrP23-144 and huPrP23-144 fibrils represented by a central slice perpendicular to the fibril axis. Polymorph 1 of moPrP23-144 fibrils (red) showed the same fold as that in huPrP23-144 fibrils (purple). Polymorph 2 of moPrP23-144 fibrils (green) showed a distinctly different fold. e-f, An atomic model built based on the map for polymorph 1 of moPrP23-144 fibrils, with a map resolution of 3.92 Å and model resolution of 4.49 Å. The backbone fold in this model is identical to that in huPrP23-144 fibrils. The structure of polymorph 2 of moPrP23-144 fibrils could not be determined due to poor quality of cryo-EM data for this polymorphic form.

Extended Data Fig. 6 The structural model illustrating seeding reaction at the top end of huPrP23-144 fibrils in the presence of huPrP23-144 and ShaPrP23-144 substrates.

Two representative protofilaments (A and B) are shown only. a, Top and side views of a preformed huPrP23-144 fibril (seed) with solvent-exposed hydrophobic side chains shown in blue. b, Top view of a preformed huPrP23-144 fibril (grey) with a newly recruited and converted subunit of huPrP23-144 (orange). c, Top view of a preformed huPrP23-144 fibril (grey) with a newly recruited subunit of ShaPrP23-144 (red). Adaptation of ShaPrP23-144 to the structure of huPrP23-144 seed would lead to significant intermolecular steric clashes between bulky, elongated side chains of M112 and M139 (as indicated by the yellow star), explaining a cross-seeding barrier.

Extended Data Fig. 7 The structural model illustrating seeding reaction at the bottom end of huPrP23-144 fibrils in the presence of huPrP23-144 and ShaPrP23-144 substrates.

Two representative protofilaments (A and B) are shown for illustrative purposes. a, Bottom and side views of a preformed huPrP23-144 fibril (seed) with solvent-exposed hydrophobic side chains shown in blue. b, Bottom view of a preformed huPrP23-144 fibril (grey) with a newly recruited (to protofilament A) and converted subunit of huPrP23-144 (orange). c, Bottom view of a preformed huPrP23-144 fibril (grey) with a newly recruited (to protofilament A) and converted first subunit of ShaPrP23-144 (red). Due to non-planar structure, C-terminal hydrophobic residues at this end of protofilament B are protruding to water. Thus, recruitment of the first ShaPrP subunit would not result in any steric clashes. d, Bottom view of a preformed huPrP23-144 fibril (grey) with a second newly recruited (to protofilament B) and converted subunit of huPrP23-144 (orange). e, Bottom view of a preformed huPrP23-144 fibril (grey) with a second recruited (to protofilament B) subunit of ShaPrP23-144 (red). Adaptation of this subunit to the structure of the huPrP23-144 seed would lead to intermolecular steric clashes between side chains of M139 and M112 (as indicated by the yellow star), explaining a cross-seeding barrier.

Extended Data Fig. 8 The backbone cryo-EM structures of PrP amyloid fibrils including recombinant huPrP23-144 fibrils determined herein (a, PDB 7RL4), recombinant huPrP94-178 fibrils20 (b, PDB 6UUR), brain-derived 263 K prions18 (c, PDB 7LNA), recombinant huPrP23-231 fibrils16 (d, PDB 6LNI), and recombinant E196K huPrP23-231 fibrils17 (e, PDB 7DWV).

The core of huPrP23-144 fibrils is marked as red.

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Li, Q., Jaroniec, C.P. & Surewicz, W.K. Cryo-EM structure of disease-related prion fibrils provides insights into seeding barriers. Nat Struct Mol Biol 29, 962–965 (2022). https://doi.org/10.1038/s41594-022-00833-4

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