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- EMDB-1187: Elongated oligomers assemble into mammalian PrP amyloid fibrils. -

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Basic information

Entry
Database: EMDB / ID: EMD-1187
TitleElongated oligomers assemble into mammalian PrP amyloid fibrils.
Map dataVolume (map) file of a Mouse PrP amyloid fibril (900 Angstrom helical crossover repeat).
Sample
  • Sample: Mouse Prion Protein PrP - residue 91-231
  • Protein or peptide: Mouse Prion Protein
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsTattum MH / Cohen-Krausz S / Khalili-shirazi A / Jackson GS / Orlova EV / Collinge J / Clarke AR / Saibil HR
CitationJournal: J Mol Biol / Year: 2006
Title: Elongated oligomers assemble into mammalian PrP amyloid fibrils.
Authors: M Howard Tattum / Sara Cohen-Krausz / Kanjana Thumanu / Christopher W Wharton / Azadeh Khalili-Shirazi / Graham S Jackson / Elena V Orlova / John Collinge / Anthony R Clarke / Helen R Saibil /
Abstract: In prion diseases, the mammalian prion protein PrP is converted from a monomeric, mainly alpha-helical state into beta-rich amyloid fibrils. To examine the structure of the misfolded state, amyloid ...In prion diseases, the mammalian prion protein PrP is converted from a monomeric, mainly alpha-helical state into beta-rich amyloid fibrils. To examine the structure of the misfolded state, amyloid fibrils were grown from a beta form of recombinant mouse PrP (residues 91-231). The beta-PrP precursors assembled slowly into amyloid fibrils with an overall helical twist. The fibrils exhibit immunological reactivity similar to that of ex vivo PrP Sc. Using electron microscopy and image processing, we obtained three-dimensional density maps of two forms of PrP fibrils with slightly different twists. They reveal two intertwined protofilaments with a subunit repeat of approximately 60 A. The repeating unit along each protofilament can be accounted for by elongated oligomers of PrP, suggesting a hierarchical assembly mechanism for the fibrils. The structure reveals flexible crossbridges between the two protofilaments, and subunit contacts along the protofilaments that are likely to reflect specific features of the PrP sequence, in addition to the generic, cross-beta amyloid fold.
History
DepositionFeb 1, 2006-
Header (metadata) releaseFeb 2, 2006-
Map releaseMay 9, 2006-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016713403
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016713403
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1187.gif

Downloads & links

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Map

FileDownload / File: emd_1187.map.gz / Format: CCP4 / Size: 618.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume (map) file of a Mouse PrP amyloid fibril (900 Angstrom helical crossover repeat).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.2 Å/pix.
x 101 pix.
= 525.2 Å		5.2 Å/pix.
x 40 pix.
= 208. Å		5.2 Å/pix.
x 40 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.2 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0155 / Movie #1: 0.0167134
Minimum - Maximum-0.00465072 - 0.0197981
Average (Standard dev.)0.00156821 (±0.00566669)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions4040101
Spacing4040101
CellA: 208 Å / B: 208 Å / C: 525.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z4040101
origin x/y/z0.0000.0000.000
length x/y/z208.000208.000525.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS4040101
D min/max/mean-0.0050.0200.002

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Supplemental data

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Sample components

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Entire : Mouse Prion Protein PrP - residue 91-231

EntireName: Mouse Prion Protein PrP - residue 91-231
Components
  • Sample: Mouse Prion Protein PrP - residue 91-231
  • Protein or peptide: Mouse Prion Protein

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Supramolecule #1000: Mouse Prion Protein PrP - residue 91-231

SupramoleculeName: Mouse Prion Protein PrP - residue 91-231 / type: sample / ID: 1000 / Oligomeric state: Amyloid fibril / Number unique components: 1

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Macromolecule #1: Mouse Prion Protein

MacromoleculeName: Mouse Prion Protein / type: protein_or_peptide / ID: 1 / Name.synonym: Mo PrP / Details: Recombinant protein expressed in E.coli / Oligomeric state: multimeric amyloid fibril / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House Mouse
Molecular weightExperimental: 171.95 KDa / Theoretical: 171.95 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pTrcHisB

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 3 / Details: 10mM Tris, 10mM Sodium Acetate
StainingType: NEGATIVE
Details: 3ul sample applied to grid for 2-3 minutes before blotting. 3ul 2% uranyl acetate added and blotted after 3 minutes.
GridDetails: 300 mesh copper grid
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeFEI TECNAI 10
TemperatureAverage: 293 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 150,000 magnification
DetailsLow Dose. FEI TECNAI 10 microscope. Gatan single tilt negative stain holder.
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 477 / Average electron dose: 10 e/Å2 / Od range: 2.5 / Bits/pixel: 8
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 27000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER

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Image processing

DetailsParticles were selected manually.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: Crossover repeats of the disordered helical fibrils were treated as single particles
Number images used: 477
Final two d classificationNumber classes: 1

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