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- EMDB-19461: Alpha-synuclein amyloid fibrils with WT DNAJB1 -

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Basic information

Entry
Database: EMDB / ID: EMD-19461
TitleAlpha-synuclein amyloid fibrils with WT DNAJB1
Map dataPostprocessed map of the complex formed of alpha-synuclein amyloid fibrils and WT DNAJB1
Sample
  • Complex: Alpha-synuclein amyloid fibril with WT DNAJB1
KeywordsChaperones / amyloid fibril / disaggregation / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 11.16 Å
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 23, 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_19461.png

Downloads & links

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Map

FileDownload / File: emd_19461.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of the complex formed of alpha-synuclein amyloid fibrils and WT DNAJB1
Voxel sizeX=Y=Z: 3.575 Å
Density
Contour LevelBy AUTHOR: 0.0042
Minimum - Maximum-0.033168305 - 0.046475124
Average (Standard dev.)0.00017453622 (±0.0020857705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 457.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19461_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map #1 of the complex formed...

Fileemd_19461_half_map_1.map
AnnotationUnfiltered half map #1 of the complex formed of alpha-synuclein amyloid fibrils and WT DNAJB1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map #2 of the complex formed...

Fileemd_19461_half_map_2.map
AnnotationUnfiltered half map #2 of the complex formed of alpha-synuclein amyloid fibrils and WT DNAJB1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Alpha-synuclein amyloid fibril with WT DNAJB1

EntireName: Alpha-synuclein amyloid fibril with WT DNAJB1
Components
  • Complex: Alpha-synuclein amyloid fibril with WT DNAJB1

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Supramolecule #1: Alpha-synuclein amyloid fibril with WT DNAJB1

SupramoleculeName: Alpha-synuclein amyloid fibril with WT DNAJB1 / 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
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPESHEPES
2.0 mMDTTDL-1,4-Dithiothreitol
GridModel: C-flat-2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: relion_helix_inimodel2d using fibre crossover distance
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 40.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -7.2 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 11.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199136

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