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- EMDB-19441: Alpha-synuclein amyloid fibrils with DNAJB1-Helix V mutant, HSC70... -

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Basic information

Entry
Database: EMDB / ID: EMD-19441
TitleAlpha-synuclein amyloid fibrils with DNAJB1-Helix V mutant, HSC70, HSP110 and ATP
Map dataTomogram of alpha-synuclein amyloid fibrils incubated with a mutant of DNAJB1 mutated in helix V, HSC70, HSP110 and ATP
Sample
  • Complex: Alpha-synuclein amyloid fibrils incubated with a helix V mutant of DNAJB1, HSC70, HSP110 and ATP
KeywordsChaperones / amyloid fibril / disaggregation / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsSaibil HR / Monistrol J
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
Wellcome Trust106249/Z/14/Z United Kingdom
CitationJournal: Biorxiv / Year: 2024
Title: Stepwise recruitment of Hsc70 by DNAJB1 produces ordered arrays primed for bursts of amyloid fibre disassembly
Authors: Monistrol J / Beton JG / Johnston EC / Saibil HR
History
DepositionJan 18, 2024-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19441.png

Downloads & links

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Map

FileDownload / File: emd_19441.map.gz / Format: CCP4 / Size: 6.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of alpha-synuclein amyloid fibrils incubated with a mutant of DNAJB1 mutated in helix V, HSC70, HSP110 and ATP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.8 Å/pix.
x 458 pix.
= 1740.4 Å		3.8 Å/pix.
x 1933 pix.
= 7345.4 Å		3.8 Å/pix.
x 2036 pix.
= 7736.8 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 3.8 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-7193.98700000000008 - 3969.747800000000097
Average (Standard dev.)37.910589999999999 (±306.393950000000018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin8018389
Dimensions19332036458
Spacing20361933458
CellA: 7736.8 Å / B: 7345.4 Å / C: 1740.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Alpha-synuclein amyloid fibrils incubated with a helix V mutant o...

EntireName: Alpha-synuclein amyloid fibrils incubated with a helix V mutant of DNAJB1, HSC70, HSP110 and ATP
Components
  • Complex: Alpha-synuclein amyloid fibrils incubated with a helix V mutant of DNAJB1, HSC70, HSP110 and ATP

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Supramolecule #1: Alpha-synuclein amyloid fibrils incubated with a helix V mutant o...

SupramoleculeName: Alpha-synuclein amyloid fibrils incubated with a helix V mutant of DNAJB1, HSC70, HSP110 and ATP
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPESHEPES
50.0 mMKClPotassium chloride
5.0 mMMgClMagnesium chloride
5.0 mMATPAdenosine triphosphate
2.0 mMDTTDL-1,4-Dithiothreitol
6.0 mMPEPPhosphoenolpyruvate
20.0 ng/uLpyruvate kinase
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber temperature: 277.15 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: EMS / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
DetailsNote: the original pixel size for the tomogram recording was 1.94 A/pixel. This was subsequently rounded to 1.9 A/pixel and the 2x binned tomogram deposited here is listed as 3.8 A/pixel.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 116.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.4 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: RELION (ver. 4) / Number images used: 121

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