- EMDB-30887: Cryo-EM structure of amyloid fibril formed by familial prion dise... -
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Basic information
Entry
Database: EMDB / ID: EMD-30887
Title
Cryo-EM structure of amyloid fibril formed by familial prion disease-related mutation E196K
Map data
Masked density map
Sample
Organelle or cellular component: Human prion E196K mutation amyloid fibril
Protein or peptide: Major prion protein
Function / homology
Function and homology information
positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production ...positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / NCAM1 interactions / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of interleukin-2 production / extrinsic component of membrane / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / regulation of peptidyl-tyrosine phosphorylation / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / response to cadmium ion / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / positive regulation of protein localization to plasma membrane / tubulin binding / molecular condensate scaffold activity / negative regulation of protein phosphorylation / molecular function activator activity / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to xenobiotic stimulus / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / nuclear membrane / microtubule binding / protease binding / response to oxidative stress / transmembrane transporter binding / postsynapse / learning or memory / molecular adaptor activity / postsynaptic density / regulation of cell cycle / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / Golgi apparatus / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain Similarity search - Domain/homology
Journal: Sci Adv / Year: 2021 Title: Genetic prion disease-related mutation E196K displays a novel amyloid fibril structure revealed by cryo-EM. Authors: Li-Qiang Wang / Kun Zhao / Han-Ye Yuan / Xiang-Ning Li / Hai-Bin Dang / Yeyang Ma / Qiang Wang / Chen Wang / Yunpeng Sun / Jie Chen / Dan Li / Delin Zhang / Ping Yin / Cong Liu / Yi Liang / Abstract: Prion diseases are caused by the conformational conversion of prion protein (PrP). Forty-two different mutations were identified in human PrP, leading to genetic prion diseases with distinct clinical ...Prion diseases are caused by the conformational conversion of prion protein (PrP). Forty-two different mutations were identified in human PrP, leading to genetic prion diseases with distinct clinical syndromes. Here, we report the cryo–electron microscopy structure of an amyloid fibril formed by full-length human PrP with E196K mutation, a genetic Creutzfeldt-Jakob disease–related mutation. This mutation disrupts key interactions in the wild-type PrP fibril, forming an amyloid fibril with a conformation distinct from the wild-type PrP fibril and hamster brain–derived prion fibril. The E196K fibril consists of two protofibrils. Each subunit forms five β strands stabilized by a disulfide bond and an unusual hydrophilic cavity stabilized by a salt bridge. Four pairs of amino acids from opposing subunits form four salt bridges to stabilize the zigzag interface of the two protofibrils. Our results provide structural evidences of the diverse prion strains and highlight the importance of familial mutations in inducing different strains.
History
Deposition
Jan 18, 2021
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Header (metadata) release
Oct 13, 2021
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Map release
Oct 13, 2021
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Update
Oct 13, 2021
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Current status
Oct 13, 2021
Processing site: PDBj / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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