EMDB-23459: Infectious mammalian prion fibril (263K scrapie)

Basic information

• Entry: Database: EMDB / ID: EMD-23459
• Title: Infectious mammalian prion fibril (263K scrapie)

Sample

• Complex: infectious mammalian prion fibril (263K scrapie)
  • Protein or peptide: Major prion protein

Function / homology

Function:

regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / : / negative regulation of type II interferon production / positive regulation of protein targeting to membrane / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / negative regulation of protein phosphorylation / molecular condensate scaffold activity / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / terminal bouton / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / amyloid fibril formation / learning or memory / regulation of cell cycle / membrane raft / cell cycle / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol

Domain/homology:

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

Component:

Major prion protein

• Biological species: Mesocricetus auratus (golden hamster) / Golden hamster (golden hamster)
• Method: single particle reconstruction / cryo EM / Resolution: 3.14 Å
• Authors: Kraus A / Hoyt F / Schwartz CL / Hansen B / Hughson AG / Artikis E / Race B / Caughey B

Funding support

United States, 2 items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI000580	United States
Other private		United States

• Citation: Journal: Mol Cell / Year: 2021; Title: High-resolution structure and strain comparison of infectious mammalian prions.; Authors: Allison Kraus / Forrest Hoyt / Cindi L Schwartz / Bryan Hansen / Efrosini Artikis / Andrew G Hughson / Gregory J Raymond / Brent Race / Gerald S Baron / Byron Caughey / ; Abstract: Within the extensive range of self-propagating pathologic protein aggregates of mammals, prions are the most clearly infectious (e.g., ∼10 lethal doses per milligram). The structures of such lethal assemblies of PrP molecules have been poorly understood. Here we report a near-atomic core structure of a brain-derived, fully infectious prion (263K strain). Cryo-electron microscopy showed amyloid fibrils assembled with parallel in-register intermolecular β sheets. Each monomer provides one rung of the ordered fibril core, with N-linked glycans and glycolipid anchors projecting outward. Thus, single monomers form the templating surface for incoming monomers at fibril ends, where prion growth occurs. Comparison to another prion strain (aRML) revealed major differences in fibril morphology but, like 263K, an asymmetric fibril cross-section without paired protofilaments. These findings provide structural insights into prion propagation, strains, species barriers, and membrane pathogenesis. This structure also helps frame considerations of factors influencing the relative transmissibility of other pathologic amyloids.

History

Deposition	Feb 6, 2021	-
Header (metadata) release	Sep 1, 2021	-
Map release	Sep 1, 2021	-
Update	Nov 17, 2021	-
Current status	Nov 17, 2021	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_23459.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.09 Å

Density

Contour Level	By AUTHOR: 0.01 / Movie #1: 0.015
Minimum - Maximum	-0.05712004 - 0.10128823
Average (Standard dev.)	3.1214844e-05 (±0.0013481894)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 340 340 340 Spacing 340 340 340
Cell	A=B=C: 370.6 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.09	1.09	1.09
M x/y/z	340	340	340
origin x/y/z	0.000	0.000	0.000
length x/y/z	370.600	370.600	370.600
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	340	340	340
D min/max/mean	-0.057	0.101	0.000

Supplemental data

Half map: #2

• File: emd_23459_half_map_1.map

Half map: #1

• File: emd_23459_half_map_2.map

Sample components

Entire : infectious mammalian prion fibril (263K scrapie)

• Entire: Name: infectious mammalian prion fibril (263K scrapie)

Components

• Complex: infectious mammalian prion fibril (263K scrapie)
  • Protein or peptide: Major prion protein

Supramolecule #1: infectious mammalian prion fibril (263K scrapie)

• Supramolecule: Name: infectious mammalian prion fibril (263K scrapie) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all; Details: Purified from brains of hamsters with clinical scrapie prion disease.
• Source (natural): Organism: Mesocricetus auratus (golden hamster) / Organ: brain / Tissue: brain

Macromolecule #1: Major prion protein

• Macromolecule: Name: Major prion protein / type: protein_or_peptide / ID: 1 ; Details: Protease-resistant glycosylated, glycophophatidlyinositol-anchored infectious prion amyloid core (inclusive of residues 90-231).; Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Golden hamster (golden hamster) / Organ: brain
• Molecular weight: Theoretical: 16.264101 KDa

Sequence

String:

GQGGGTHNQW NKPSKPKTNM KHMAGAAAAG AVVGGLGGYM LGSAMSRPMM HFGNDWEDRY YRENMNRYPN QVYYRPVDQY NNQNNFVHD CVNITIKQHT VTTTTKGENF TETDIKIMER VVEQMCTTQY QKESQAYYDG RRS

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: filament

Sample preparation

• Buffer: pH: 7.4
• Grid: Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.07200000000000001 kPa / Details: Solarus 950 (Gatan, Pleasanton CA)
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: OTHER / Imaging mode: BRIGHT FIELD
• Sample stage: Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Details: Processing and reconstruction was conducted in Relion as per Scheres, Acta Cryst. (2020). D76, 94-101
• Particle selection: Number selected: 337368 ; Details: Filament start and end positions were picked manually in RELION. Particles were extracted with an interbox distance of 14.7A along the filament axis.
• CTF correction: Software - Name: CTFFIND (ver. 4.1)
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1); Software - details: RELION was used for 2D and 3D classification of particles, refinement, Bayesian polishing and post-processing with a soft-edged mask.; Details: Auto-refinement was then performed while optimizing the helical twist and rise. Auto-refinement with refinement of twist and rise yielded a final map with a twist of -0.847 degree and rise of 4.874 angstrom. Iterative cycles of CTF refinement, Bayesian polishing, and auto refinement were used until resolution estimates stabilized. Post processing in RELION was performed with a soft-edged mask representing 10% of the central Z length of the fibril. Sharpening was applied with a B-factor of -31 square angstrom.; Number images used: 15884
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
• Final 3D classification: Software - Name: RELION (ver. 3.1)

Atomic model buiding 1

• Refinement: Space: RECIPROCAL / Protocol: AB INITIO MODEL

Output model

PDB-7lna:
Infectious mammalian prion fibril (263K scrapie)