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- EMDB-28089: a22L prion fibril -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-28089
Titlea22L prion fibril
Map dataPost processed, real space averaged map of anchorless 22L prion fibril
Sample
  • Complex: GPI anchorless underglycosylated 22L prion fibril
    • Protein or peptide: Major prion protein
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / negative regulation of dendritic spine maintenance / cupric ion binding / regulation of potassium ion transmembrane transport / response to copper ion / nucleobase-containing compound metabolic process / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production / activation of protein kinase activity / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / cuprous ion binding / 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 / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / negative regulation of DNA-binding transcription factor activity / 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 / regulation of protein localization / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / protease binding / nuclear membrane / response to oxidative stress / transmembrane transporter binding / molecular adaptor activity / postsynaptic density / learning or memory / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / 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 speciesMus musculus (house mouse) / house mouse (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHoyt F / Caughey B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI000580-33 United States
CitationJournal: PLoS Pathog / Year: 2022
Title: Cryo-EM of prion strains from the same genotype of host identifies conformational determinants.
Authors: Forrest Hoyt / Parvez Alam / Efrosini Artikis / Cindi L Schwartz / Andrew G Hughson / Brent Race / Chase Baune / Gregory J Raymond / Gerald S Baron / Allison Kraus / Byron Caughey /
Abstract: Prion strains in a given type of mammalian host are distinguished by differences in clinical presentation, neuropathological lesions, survival time, and characteristics of the infecting prion protein ...Prion strains in a given type of mammalian host are distinguished by differences in clinical presentation, neuropathological lesions, survival time, and characteristics of the infecting prion protein (PrP) assemblies. Near-atomic structures of prions from two host species with different PrP sequences have been determined but comparisons of distinct prion strains of the same amino acid sequence are needed to identify purely conformational determinants of prion strain characteristics. Here we report a 3.2 Å resolution cryogenic electron microscopy-based structure of the 22L prion strain purified from the brains of mice engineered to express only PrP lacking glycophosphatidylinositol anchors [anchorless (a) 22L]. Comparison of this near-atomic structure to our recently determined structure of the aRML strain propagated in the same inbred mouse reveals that these two mouse prion strains have distinct conformational templates for growth via incorporation of PrP molecules of the same sequence. Both a22L and aRML are assembled as stacks of PrP molecules forming parallel in-register intermolecular β-sheets and intervening loops, with single monomers spanning the ordered fibril core. Each monomer shares an N-terminal steric zipper, three major arches, and an overall V-shape, but the details of these and other conformational features differ markedly. Thus, variations in shared conformational motifs within a parallel in-register β-stack fibril architecture provide a structural basis for prion strain differentiation within a single host genotype.
History
DepositionSep 9, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28089.png

Downloads & links

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Map

FileDownload / File: emd_28089.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost processed, real space averaged map of anchorless 22L prion fibril
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 401.28 Å		1.05 Å/pix.
x 384 pix.
= 401.28 Å		1.05 Å/pix.
x 384 pix.
= 401.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.023766868 - 0.050889917
Average (Standard dev.)0.00017263262 (±0.0017125767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 401.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map for anchorless 22L prion fibril

Fileemd_28089_half_map_1.map
AnnotationEM half map for anchorless 22L prion fibril
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map for anchorless 22L prion fibril

Fileemd_28089_half_map_2.map
AnnotationEM half map for anchorless 22L prion fibril
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPI anchorless underglycosylated 22L prion fibril

EntireName: GPI anchorless underglycosylated 22L prion fibril
Components
  • Complex: GPI anchorless underglycosylated 22L prion fibril
    • Protein or peptide: Major prion protein

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Supramolecule #1: GPI anchorless underglycosylated 22L prion fibril

SupramoleculeName: GPI anchorless underglycosylated 22L prion fibril / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse) / Organ: Brain

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Macromolecule #1: Major prion protein

MacromoleculeName: Major prion protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: house mouse (house mouse)
Molecular weightTheoretical: 25.550348 KDa
SequenceString: MANLGYWLLA LFVTMWTDVG LCKKRPKPGG WNTGGSRYPG QGSPGGNRYP PQGGTWGQPH GGGWGQPHGG SWGQPHGGSW GQPHGGGWG QGGGTHNQWN KPSKPKTNLK HVAGAAAAGA VVGGLGGYML GSAMSRPMIH FGNDWEDRYY RENMYRYPNQ V YYRPVDQY ...String:
MANLGYWLLA LFVTMWTDVG LCKKRPKPGG WNTGGSRYPG QGSPGGNRYP PQGGTWGQPH GGGWGQPHGG SWGQPHGGSW GQPHGGGWG QGGGTHNQWN KPSKPKTNLK HVAGAAAAGA VVGGLGGYML GSAMSRPMIH FGNDWEDRYY RENMYRYPNQ V YYRPVDQY SNQNNFVHDC VNITIKQHTV TTTTKGENFT ETDVKMMERV VEQMCVTQYQ KESQAYYDGR RSS

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
Details: Sample suspended in 20 mM Tris pH 7.4, 100 mM containing 0.02% amphipol 8-35
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 4449 / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.75 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.565 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0 beta)
Details: Pixel size was corrected in post processing from 1.1 A/pix to 1.045 A/pix to correct an error in the reported magnification pixel size.
Number images used: 16409
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Segment selectionNumber selected: 226306
Startup modelType of model: OTHER
Details: Starting model was generated from 2D classes using relion_helix_inimodel2d
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4.0 beta)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8efu:
a22L prion fibril

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