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- EMDB-46904: AD-fold Quadruple Helical Filament Polymorph -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-46904
TitleAD-fold Quadruple Helical Filament Polymorph
Map data
Sample
  • Complex: Truncated tau 297-391
Keywords297-391 Truncated Tau 200mM MgCl2 10mM Phosphate Buffer 10mM DTT / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsVaquer-Alicea J / Kunach P / Diamond MI
Funding support United States, 3 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1RF1AG065407-01A1 United States
Chan Zuckerberg Initiative2018-191983 (5022) United States
CitationJournal: To Be Published
Title: AD-fold Quadruple Helical Filament Polymorph
Authors: Vaquer-Alicea J / Kunach P / Diamond MI
History
DepositionSep 5, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 8, 2025-
Current statusJan 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46904.png

Downloads & links

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Map

FileDownload / File: emd_46904.map.gz / Format: CCP4 / Size: 17.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 39 pix.
= 32.37 Å		0.83 Å/pix.
x 340 pix.
= 282.2 Å		0.83 Å/pix.
x 340 pix.
= 282.2 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: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.031219669 - 0.06197767
Average (Standard dev.)0.00019321921 (±0.0029346175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00144
Dimensions34034039
Spacing34034039
CellA: 282.19998 Å / B: 282.19998 Å / C: 32.37 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46904_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_46904_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46904_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46904_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Truncated tau 297-391

EntireName: Truncated tau 297-391
Components
  • Complex: Truncated tau 297-391

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Supramolecule #1: Truncated tau 297-391

SupramoleculeName: Truncated tau 297-391 / 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

Concentration10 mg/mL
BufferpH: 7.4 / Details: 10mM Phosphate Buffer 10mM DTT 200mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.749 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.814 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 80078
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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