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- EMDB-0931: Cryo-EM structure of amyloid fibril formed by full-length human p... -

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Basic information

Entry
Database: EMDB / ID: EMD-0931
TitleCryo-EM structure of amyloid fibril formed by full-length human prion protein
Map data
Sample
  • Organelle or cellular component: human prion protein amyloid fibril
    • Protein or peptide: Major prion protein
Function / homology
Function and homology information


: / 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 / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport ...: / 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 / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / response to amyloid-beta / : / negative regulation of type II interferon production / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / negative regulation of long-term synaptic potentiation / positive regulation of protein tyrosine kinase activity / long-term memory / response to cadmium ion / inclusion body / regulation of peptidyl-tyrosine phosphorylation / cellular response to copper ion / neuron projection maintenance / molecular condensate scaffold activity / tubulin binding / protein sequestering activity / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / postsynapse / microtubule binding / nuclear membrane / response to oxidative stress / protease binding / transmembrane transporter binding / postsynaptic density / learning or memory / molecular adaptor activity / regulation of cell cycle / cell cycle / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
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
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.702 Å
AuthorsWang LQ / Zhao K / Yuan HY / Wang Q / Guan ZY / Tao J / Li XN / Hao MM / Chen J / Zhang DL ...Wang LQ / Zhao K / Yuan HY / Wang Q / Guan ZY / Tao J / Li XN / Hao MM / Chen J / Zhang DL / Zhu HL / Yin P / Liu C / Liang Y
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cryo-EM structure of an amyloid fibril formed by full-length human prion protein.
Authors: Li-Qiang Wang / Kun Zhao / Han-Ye Yuan / Qiang Wang / Zeyuan Guan / Jing Tao / Xiang-Ning Li / Yunpeng Sun / Chuan-Wei Yi / Jie Chen / Dan Li / Delin Zhang / Ping Yin / Cong Liu / Yi Liang /
Abstract: Prion diseases are caused by the misfolding of prion protein (PrP). Misfolded PrP forms protease-resistant aggregates in vivo (PrP) that are able to template the conversion of the native form of the ...Prion diseases are caused by the misfolding of prion protein (PrP). Misfolded PrP forms protease-resistant aggregates in vivo (PrP) that are able to template the conversion of the native form of the protein (PrP), a property shared by in vitro-produced PrP fibrils. Here we produced amyloid fibrils in vitro from recombinant, full-length human PrP (residues 23-231) and determined their structure using cryo-EM, building a model for the fibril core comprising residues 170-229. The PrP fibril consists of two protofibrils intertwined in a left-handed helix. Lys194 and Glu196 from opposing subunits form salt bridges, creating a hydrophilic cavity at the interface of the two protofibrils. By comparison with the structure of PrP, we propose that two α-helices in the C-terminal domain of PrP are converted into β-strands stabilized by a disulfide bond in the PrP fibril. Our data suggest that different PrP mutations may play distinct roles in modulating the conformational conversion.
History
DepositionDec 30, 2019-
Header (metadata) releaseJun 10, 2020-
Map releaseJun 10, 2020-
UpdateJun 24, 2020-
Current statusJun 24, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lni
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6lni
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0931.png

Downloads & links

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Map

FileDownload / File: emd_0931.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.050022557 - 0.11823607
Average (Standard dev.)0.00020733173 (±0.0033544828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 405.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z405.600405.600405.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0500.1180.000

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Supplemental data

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Sample components

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Entire : human prion protein amyloid fibril

EntireName: human prion protein amyloid fibril
Components
  • Organelle or cellular component: human prion protein amyloid fibril
    • Protein or peptide: Major prion protein

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Supramolecule #1: human prion protein amyloid fibril

SupramoleculeName: human prion protein amyloid fibril / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Major prion protein

MacromoleculeName: Major prion protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.996355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKRPKPGGW NTGGSRYPGQ GSPGGNRYPP QGGGGWGQPH GGGWGQPHGG GWGQPHGGGW GQPHGGGWGQ GGGTHSQWNK PSKPKTNMK HMAGAAAAGA VVGGLGGYML GSAMSRPIIH FGSDYEDRYY RENMHRYPNQ VYYRPMDEYS NQNNFVHDCV N ITIKQHTV ...String:
MKKRPKPGGW NTGGSRYPGQ GSPGGNRYPP QGGGGWGQPH GGGWGQPHGG GWGQPHGGGW GQPHGGGWGQ GGGTHSQWNK PSKPKTNMK HMAGAAAAGA VVGGLGGYML GSAMSRPIIH FGSDYEDRYY RENMHRYPNQ VYYRPMDEYS NQNNFVHDCV N ITIKQHTV TTTTKGENFT ETDVKMMERV VEQMCITQYE RESQAYYQRG SS

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 2.403 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.449 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.702 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86012
FSC plot (resolution estimation)

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