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- EMDB-3743: Straight filament in Alzheimer's disease brain -

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Basic information

Entry
Database: EMDB / ID: 3743
TitleStraight filament in Alzheimer's disease brain
Map data
SampleTau
  • Microtubule-associated protein tauTau protein
Function / homologyCaspase-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 / Microtubule associated protein, tubulin-binding repeat / positive regulation of diacylglycerol kinase activity / plus-end-directed organelle transport along microtubule / neurofibrillary tangle assembly / axonal transport ...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 / Microtubule associated protein, tubulin-binding repeat / positive regulation of diacylglycerol kinase activity / plus-end-directed organelle transport along microtubule / neurofibrillary tangle assembly / axonal transport / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / regulation of chromosome organization / rRNA metabolic process / negative regulation of mitochondrial membrane potential / regulation of long term synaptic depression / tubulin complex / axon development / microtubule lateral binding / negative regulation of mitochondrial fission / microtubule polymerization / generation of neurons / lipoprotein particle binding / positive regulation of cellular protein localization / axonal transport of mitochondrion / negative regulation of tubulin deacetylation / intracellular distribution of mitochondria / AT DNA binding / regulation of mitochondrial fission / central nervous system neuron development / regulation of calcium-mediated signaling / somatodendritic compartment / negative regulation of kinase activity / cellular response to brain-derived neurotrophic factor stimulus / internal protein amino acid acetylation / regulation of microtubule polymerization / receptor ligand activity / dynactin binding / regulation of microtubule polymerization or depolymerization / supramolecular fiber organization / axolemma / stress granule assembly / cytoplasmic microtubule organization / main axon / regulation of response to DNA damage stimulus / synapse assembly / microtubule associated complex / positive regulation of axon extension / phosphatidylinositol binding / axon cytoplasm / protein phosphatase 2A binding / apolipoprotein binding / regulation of microtubule cytoskeleton organization / microglial cell activation / positive regulation of microtubule polymerization / nuclear periphery / synapse organization / amyloid fibril formation / regulation of autophagy / microtubule cytoskeleton organization / astrocyte activation / cellular response to nerve growth factor stimulus / cytoplasmic ribonucleoprotein granule / regulation of synaptic plasticity / Hsp90 protein binding / memory / positive regulation of superoxide anion generation / response to lead ion / protein binding, bridging / microtubule cytoskeleton / cellular response to reactive oxygen species / cell body / cellular response to heat / regulation of cellular response to heat / neuron projection development / single-stranded DNA binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / growth cone / SH3 domain binding / positive regulation of neuron death / learning or memory / double-stranded DNA binding / actin binding / chaperone binding / cell-cell signaling / protein complex oligomerization / microtubule / protein homooligomerization / microtubule binding / dendritic spine / negative regulation of gene expression / sequence-specific DNA binding / nuclear speck / axon / neuronal cell body / dendrite / intracellular
Function and homology information
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 3.4 Å resolution
AuthorsFitzpatrick AWP / Falcon B / He S
CitationJournal: Nature / Year: 2017
Title: Cryo-EM structures of tau filaments from Alzheimer's disease.
Authors: Anthony W P Fitzpatrick / Benjamin Falcon / Shaoda He / Alexey G Murzin / Garib Murshudov / Holly J Garringer / R Anthony Crowther / Bernardino Ghetti / Michel Goedert / Sjors H W Scheres
Validation ReportPDB-ID: 5o3t

SummaryFull reportAbout validation report
DateDeposition: May 24, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Jul 26, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5o3t
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3743.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:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.07519699 - 0.139756
Average (Standard dev.)0.00013582216 (0.002800759)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions270270270
Origin000
Limit269269269
Spacing270270270
CellA=B=C: 280.8 Å
α=β=γ: 90 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-0.0750.1400.000

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Supplemental data

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Sample components

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Entire Tau

EntireName: Tau / Number of components: 2

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Component #2: protein, Microtubule-associated protein tau

ProteinName: Microtubule-associated protein tauTau protein / Recombinant expression: No
MassTheoretical: 7.940141 kDa
SourceSpecies: Homo sapiens (human)

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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: 4.74 Å / Delta phi: -1.05 deg.
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 20 mM Tris-HCl pH 7.4 containing 100 mM NaCl
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 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: 900 - 3000 nm / Energy filter: GIF Quantum / Energy window: -10-10 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1560
Details: images were collected in movie-mode at 5 frames per second

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Fourier shell correlation / Refinement space: RECIPROCAL
Details: Fourier-space refinement of the complete atomic model against the paired helical filament and straight filament maps was performed in REFMAC. A stack of three consecutive monomers from each of the protofilaments was refined to preserve nearest-neighbour interactions for the middle chain.
Input PDB model: 2RNM
Chain ID: 2RNM_A

Overall bvalue: 114
Output model

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