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- EMDB-70184: Recombinant AD THF incubated with SW-MK-NBD (Non-Symmetric Binding) -

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Basic information

Entry
Database: EMDB / ID: EMD-70184
TitleRecombinant AD THF incubated with SW-MK-NBD (Non-Symmetric Binding)
Map dataRecombinant AD THF incubated with SW-MK-NBD (Non-Symmetric Binding)
Sample
  • Complex: Microtubule-associated protein tau
    • Protein or peptide: Microtubule-associated protein tau
KeywordsMK-6240 PET Ligand / AD PHF / PROTEIN FIBRIL / SW-MK-NBD / Amyloid Dye
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / tubulin complex / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / generation of neurons ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / tubulin complex / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / generation of neurons / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / regulation of microtubule-based movement / intracellular distribution of mitochondria / regulation of chromosome organization / central nervous system neuron development / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / microtubule polymerization / negative regulation of mitochondrial membrane potential / regulation of microtubule polymerization / dynactin binding / apolipoprotein binding / protein polymerization / main axon / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / axolemma / glial cell projection / neurofibrillary tangle assembly / positive regulation of axon extension / positive regulation of microtubule polymerization / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / positive regulation of superoxide anion generation / cellular response to brain-derived neurotrophic factor stimulus / supramolecular fiber organization / regulation of long-term synaptic depression / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / somatodendritic compartment / axon cytoplasm / synapse assembly / phosphatidylinositol binding / nuclear periphery / astrocyte activation / enzyme inhibitor activity / protein phosphatase 2A binding / stress granule assembly / regulation of microtubule cytoskeleton organization / regulation of autophagy / cellular response to reactive oxygen species / microglial cell activation / cellular response to nerve growth factor stimulus / Hsp90 protein binding / protein homooligomerization / SH3 domain binding / PKR-mediated signaling / regulation of synaptic plasticity / synapse organization / response to lead ion / microtubule cytoskeleton organization / memory / neuron projection development / cytoplasmic ribonucleoprotein granule / cell-cell signaling / single-stranded DNA binding / cellular response to heat / growth cone / protein-folding chaperone binding / microtubule cytoskeleton / actin binding / cell body / double-stranded DNA binding / microtubule binding / sequence-specific DNA binding / amyloid fibril formation / dendritic spine / microtubule / protein-macromolecule adaptor activity / learning or memory / neuron projection / membrane raft / negative regulation of gene expression / axon / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus
Similarity search - Function
Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / :
Similarity search - Domain/homology
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsKunach P / Diamond MI / Rosa-Neto P
Funding support United States, Canada, 4 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R35GM122481 United States
Canadian Institutes of Health Research (CIHR)MOP-11-51-31 Canada
Canadian Institutes of Health Research (CIHR)152985 Canada
CitationJournal: To Be Published
Title: Development of a tau amyloid dye from a PET ligand
Authors: Kunach P / Diamond MI
History
DepositionApr 14, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70184.png

Downloads & links

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Map

FileDownload / File: emd_70184.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRecombinant AD THF incubated with SW-MK-NBD (Non-Symmetric Binding)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 250 pix.
= 288.65 Å		1.15 Å/pix.
x 250 pix.
= 288.65 Å		1.15 Å/pix.
x 250 pix.
= 288.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1546 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.034099814 - 0.08426606
Average (Standard dev.)0.0006367375 (±0.00497008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 288.65 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70184_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_70184_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_70184_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Microtubule-associated protein tau

EntireName: Microtubule-associated protein tau
Components
  • Complex: Microtubule-associated protein tau
    • Protein or peptide: Microtubule-associated protein tau

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Supramolecule #1: Microtubule-associated protein tau

SupramoleculeName: Microtubule-associated protein tau / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Microtubule-associated protein tau

MacromoleculeName: Microtubule-associated protein tau / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.184412 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SVQIVYKPVD LSKVTSKCGS LGNIHHKPGG GQVEVKSEKL DFKDRVQSKI GSLDNITHVP GGGNKKIETH KLTFR

UniProtKB: Microtubule-associated protein tau

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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: 10 mM Phosphate buffer, pH 7.4, with 10 mM DTT and 200 mM MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 19 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.79 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.86 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 25182
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8uq7


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9o6x:
Recombinant AD THF incubated with SW-MK-NBD (Non-Symmetric Binding)

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