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- EMDB-47021: Glycosylated chronic wasting disease prion fibril -

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Basic information

Entry
Database: EMDB / ID: EMD-47021
TitleGlycosylated chronic wasting disease prion fibril
Map dataCWD density modified real-space symmetrized map
Sample
  • Complex: Naturally occurring chronic wasting disease prion fibril
    • Protein or peptide: Major prion protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPrion / Chronic Wasting Disease / Deer / Fibril / GPI-anchor / Glycosylation / PrP / Infectious / Amyloid / Brain-derived / ex vivo / Prion strain / PROTEIN FIBRIL
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / plasma membrane
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 speciesOdocoileus virginianus (white-tailed deer)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsCaughey B / Hoyt F / Alam P / Artikis E / Soukup J / Hughson A / Schwartz C / Race B / Barbian K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Acta Neuropathol / Year: 2024
Title: Cryo-EM structure of a natural prion: chronic wasting disease fibrils from deer.
Authors: Parvez Alam / Forrest Hoyt / Efrosini Artikis / Jakub Soukup / Andrew G Hughson / Cindi L Schwartz / Kent Barbian / Michael W Miller / Brent Race / Byron Caughey /
Abstract: Chronic wasting disease (CWD) is a widely distributed prion disease of cervids with implications for wildlife conservation and also for human and livestock health. The structures of infectious prions ...Chronic wasting disease (CWD) is a widely distributed prion disease of cervids with implications for wildlife conservation and also for human and livestock health. The structures of infectious prions that cause CWD and other natural prion diseases of mammalian hosts have been poorly understood. Here we report a 2.8 Å resolution cryogenic electron microscopy-based structure of CWD prion fibrils from the brain of a naturally infected white-tailed deer expressing the most common wild-type PrP sequence. Like recently solved rodent-adapted scrapie prion fibrils, our atomic model of CWD fibrils contains single stacks of PrP molecules forming parallel in-register intermolecular β-sheets and intervening loops comprising major N- and C-terminal lobes within the fibril cross-section. However, CWD fibrils from a natural cervid host differ markedly from the rodent structures in many other features, including a ~ 180° twist in the relative orientation of the lobes. This CWD structure suggests mechanisms underlying the apparent CWD transmission barrier to humans and should facilitate more rational approaches to the development of CWD vaccines and therapeutics.
History
DepositionSep 16, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47021.png

Downloads & links

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Map

FileDownload / File: emd_47021.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCWD density modified real-space symmetrized map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.106 Å		0.83 Å/pix.
x 384 pix.
= 318.106 Å		0.83 Å/pix.
x 384 pix.
= 318.106 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8284 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.2
Minimum - Maximum-15.8517685 - 41.599457000000001
Average (Standard dev.)0.010709097 (±1.1464766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.1056 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47021_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47021_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47021_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Naturally occurring chronic wasting disease prion fibril

EntireName: Naturally occurring chronic wasting disease prion fibril
Components
  • Complex: Naturally occurring chronic wasting disease prion fibril
    • Protein or peptide: Major prion protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Naturally occurring chronic wasting disease prion fibril

SupramoleculeName: Naturally occurring chronic wasting disease prion fibril
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Odocoileus virginianus (white-tailed deer) / 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: Odocoileus virginianus (white-tailed deer)
Molecular weightTheoretical: 27.965486 KDa
SequenceString: MVKSHIGSWI LVLFVAMWSD VGLCKKRPKP GGGWNTGGSR YPGQGSPGGN RYPPQGGGGW GQPHGGGWGQ PHGGGWGQPH GGGWGQPHG GGGWGQGGTH SQWNKPSKPK TNMKHVAGAA AAGAVVGGLG GYMLGSAMSR PLIHFGNDYE DRYYRENMYR Y PNQVYYRP ...String:
MVKSHIGSWI LVLFVAMWSD VGLCKKRPKP GGGWNTGGSR YPGQGSPGGN RYPPQGGGGW GQPHGGGWGQ PHGGGWGQPH GGGWGQPHG GGGWGQGGTH SQWNKPSKPK TNMKHVAGAA AAGAVVGGLG GYMLGSAMSR PLIHFGNDYE DRYYRENMYR Y PNQVYYRP VDQYNNQNTF VHDCVNITVK QHTVTTTTKG ENFTETDIKM MERVVEQMCI TQYQRESQAY YQRGASVILF SS PPVILLI SFLIFLIVG

UniProtKB: Major prion protein

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
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 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
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: 4.779 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.2913 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 7346
Segment selectionNumber selected: 535858 / Software - Name: RELION / Software - details: manual Picking
Startup modelType of model: OTHER
Details: Starting model was generated from 2D classes using relion_helix_inimodel2d
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9dmz:
Glycosylated chronic wasting disease prion fibril

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