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- EMDB-0259: Paired helical filament from sporadic Alzheimer's disease brain -

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Basic information

Entry
Database: EMDB / ID: 0259
TitlePaired helical filament from sporadic Alzheimer's disease brain
Map data
SampleTau filaments extracted from the frontotemporal cortex of a patient with sporadic Alzheimer's disease
  • Microtubule-associated protein tauTau protein
Function / homologyMicrotubule associated protein, tubulin-binding repeat / Caspase-mediated cleavage of cytoskeletal proteins / Tau and MAP proteins tubulin-binding repeat profile. / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP protein, tubulin-binding repeat / Microtubule-associated protein Tau / neurofibrillary tangle assembly / plus-end-directed organelle transport along microtubule / positive regulation of diacylglycerol kinase activity / axonal transport ...Microtubule associated protein, tubulin-binding repeat / Caspase-mediated cleavage of cytoskeletal proteins / Tau and MAP proteins tubulin-binding repeat profile. / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP protein, tubulin-binding repeat / Microtubule-associated protein Tau / neurofibrillary tangle assembly / plus-end-directed organelle transport along microtubule / positive regulation of diacylglycerol kinase activity / axonal transport / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / regulation of chromosome organization / neurofibrillary tangle / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / rRNA metabolic process / tubulin complex / negative regulation of mitochondrial membrane potential / axon development / microtubule lateral binding / generation of neurons / negative regulation of mitochondrial fission / microtubule polymerization / lipoprotein particle binding / regulation of long-term synaptic depression / positive regulation of cellular protein localization / axonal transport of mitochondrion / intracellular distribution of mitochondria / negative regulation of tubulin deacetylation / AT DNA binding / regulation of mitochondrial fission / central nervous system neuron development / glial cell projection / regulation of calcium-mediated signaling / negative regulation of kinase activity / somatodendritic compartment / internal protein amino acid acetylation / regulation of microtubule polymerization / dynactin binding / cellular response to brain-derived neurotrophic factor stimulus / regulation of microtubule polymerization or depolymerization / receptor ligand activity / stress granule assembly / axolemma / supramolecular fiber organization / cytoplasmic microtubule organization / main axon / regulation of response to DNA damage stimulus / microtubule associated complex / positive regulation of axon extension / apolipoprotein binding / regulation of microtubule cytoskeleton organization / axon cytoplasm / phosphatidylinositol binding / microglial cell activation / positive regulation of microtubule polymerization / synapse assembly / nuclear periphery / synapse organization / amyloid fibril formation / regulation of autophagy / astrocyte activation / cellular response to nerve growth factor stimulus / microtubule cytoskeleton organization / regulation of synaptic plasticity / cytoplasmic ribonucleoprotein granule / protein phosphatase 2A binding / memory / response to lead ion / positive regulation of superoxide anion generation / Hsp90 protein binding / microtubule cytoskeleton / protein binding, bridging / cellular response to reactive oxygen species / cell body / regulation of cellular response to heat / cellular response to heat / neuron projection development / single-stranded DNA binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / learning or memory / positive regulation of neuron death / SH3 domain binding / double-stranded DNA binding / growth cone / actin binding / cell-cell signaling / chaperone binding / protein complex oligomerization / microtubule binding / protein homooligomerization / microtubule / dendritic spine / negative regulation of gene expression / nuclear speck / sequence-specific DNA binding / membrane raft / axon / dendrite
Function and homology information
SourceHuman (human)
Methodhelical reconstruction / cryo EM / 3.2 Å resolution
AuthorsFalcon B / Zhang W / Schweighauser M / Murzin AG / Vidal R / Garringer HJ / Ghetti B / Scheres SHW / Goedert M
CitationJournal: Acta Neuropathol. / Year: 2018
Title: Tau filaments from multiple cases of sporadic and inherited Alzheimer's disease adopt a common fold.
Authors: Benjamin Falcon / Wenjuan Zhang / Manuel Schweighauser / Alexey G Murzin / Ruben Vidal / Holly J Garringer / Bernardino Ghetti / Sjors H W Scheres / Michel Goedert
Validation ReportPDB-ID: 6hre

SummaryFull reportAbout validation report
DateDeposition: Sep 26, 2018 / Header (metadata) release: Oct 10, 2018 / Map release: Oct 10, 2018 / Last update: Nov 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6hre
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6hre
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0259.map.gz (map file in CCP4 format, 78733 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
270 pix
1.04 Å/pix.
= 280.8 Å
270 pix
1.04 Å/pix.
= 280.8 Å
270 pix
1.04 Å/pix.
= 280.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.07166 - 0.14379393
Average (Standard dev.)0.00032994294 (0.0072139944)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions270270270
Origin0.00.00.0
Limit269.0269.0269.0
Spacing270270270
CellA=B=C: 280.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z280.800280.800280.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.0720.1440.000

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Supplemental data

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Mask #1

Fileemd_0259_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Tau filaments extracted from the frontotemporal cortex of a patie...

EntireName: Tau filaments extracted from the frontotemporal cortex of a patient with sporadic Alzheimer's disease
Number of components: 2

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Component #1: cellular-component, Tau filaments extracted from the frontotempor...

Cellular-componentName: Tau filaments extracted from the frontotemporal cortex of a patient with sporadic Alzheimer's disease
Recombinant expression: No

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Component #2: protein, Microtubule-associated protein tau

ProteinName: Microtubule-associated protein tauTau protein / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 45.919871 kDa
SourceSpecies: Human (human)
Source (natural)Organ or tissue: Brain

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Experimental details

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Sample preparation

SpecimenSpecimen state: tissue / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 2.37 Å / Delta phi: 179.45 deg.
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.2 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1700.0 - 2800.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Fourier shell correlation / Refinement space: RECIPROCAL
Details: Fourier-space refinement of the complete atomic model against the narrow Pick filament map was performed in REFMAC. A stack of three consecutive monomers was refined to preserve nearest-neighbour interactions for the middle chain.
Overall bvalue: 72.799999999999997
Output model

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