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- EMDB-43977: geranine G-induced 2N4R tau filaments -

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Basic information

Entry
Database: EMDB / ID: EMD-43977
Titlegeranine G-induced 2N4R tau filaments
Map data
Sample
  • Complex: 2N4R tau in complex with geranine G dye, its inducer
    • Protein or peptide: Isoform Tau-F of Microtubule-associated protein tau
  • Ligand: 4-hydroxy-3-{(E)-[4-(6-methyl-1,3-benzothiazol-2-yl)phenyl]diazenyl}naphthalene-2,7-disulfonic acid
Keywordsmicrotubule / amyloid / tauopathy / PROTEIN FIBRIL
Function / homologyActivation of AMPK downstream of NMDARs / PKR-mediated signaling / Isoform Tau-F of Microtubule-associated protein tau
Function and homology information
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMalyshka D / Kuret J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)F30 AG079573 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1 AG04518 United States
CitationJournal: To Be Published
Title: Submission name: Cryo-EM visualization of tau aggregation inducer-interaction sites reveals triggers of tau fibrillation and drivers of small-molecule binding
Authors: Malyshka D / Kuret J
History
DepositionMar 6, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43977.png

Downloads & links

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Map

FileDownload / File: emd_43977.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.87 Å/pix.
x 320 pix.
= 279.232 Å		0.87 Å/pix.
x 320 pix.
= 279.232 Å		0.87 Å/pix.
x 320 pix.
= 279.232 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-14.084719 - 26.640599999999999
Average (Standard dev.)-0.000000000001209 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 279.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43977_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43977_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43977_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 : 2N4R tau in complex with geranine G dye, its inducer

EntireName: 2N4R tau in complex with geranine G dye, its inducer
Components
  • Complex: 2N4R tau in complex with geranine G dye, its inducer
    • Protein or peptide: Isoform Tau-F of Microtubule-associated protein tau
  • Ligand: 4-hydroxy-3-{(E)-[4-(6-methyl-1,3-benzothiazol-2-yl)phenyl]diazenyl}naphthalene-2,7-disulfonic acid

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Supramolecule #1: 2N4R tau in complex with geranine G dye, its inducer

SupramoleculeName: 2N4R tau in complex with geranine G dye, its inducer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.4 kDa/nm

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Macromolecule #1: Isoform Tau-F of Microtubule-associated protein tau

MacromoleculeName: Isoform Tau-F of Microtubule-associated protein tau / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.919871 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEPRQEFEV MEDHAGTYGL GDRKDQGGYT MHQDQEGDTD AGLKESPLQT PTEDGSEEPG SETSDAKSTP TAEDVTAPLV DEGAPGKQA AAQPHTEIPE GTTAEEAGIG DTPSLEDEAA GHVTQARMVS KSKDGTGSDD KKAKGADGKT KIATPRGAAP P GQKGQANA ...String:
MAEPRQEFEV MEDHAGTYGL GDRKDQGGYT MHQDQEGDTD AGLKESPLQT PTEDGSEEPG SETSDAKSTP TAEDVTAPLV DEGAPGKQA AAQPHTEIPE GTTAEEAGIG DTPSLEDEAA GHVTQARMVS KSKDGTGSDD KKAKGADGKT KIATPRGAAP P GQKGQANA TRIPAKTPPA PKTPPSSGEP PKSGDRSGYS SPGSPGTPGS RSRTPSLPTP PTREPKKVAV VRTPPKSPSS AK SRLQTAP VPMPDLKNVK SKIGSTENLK HQPGGGKVQI INKKLDLSNV QSKCGSKDNI KHVPGGGSVQ IVYKPVDLSK VTS KCGSLG NIHHKPGGGQ VEVKSEKLDF KDRVQSKIGS LDNITHVPGG GNKKIETHKL TFRENAKAKT DHGAEIVYKS PVVS GDTSP RHLSNVSSTG SIDMVDSPQL ATLADEVSAS LAKQGL

UniProtKB: Isoform Tau-F of Microtubule-associated protein tau

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Macromolecule #2: 4-hydroxy-3-{(E)-[4-(6-methyl-1,3-benzothiazol-2-yl)phenyl]diazen...

MacromoleculeName: 4-hydroxy-3-{(E)-[4-(6-methyl-1,3-benzothiazol-2-yl)phenyl]diazenyl}naphthalene-2,7-disulfonic acid
type: ligand / ID: 2 / Number of copies: 3 / Formula: A1AHG
Molecular weightTheoretical: 555.603 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration2.29 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
125.0 mMNaClsodium chloride
10.0 mMC8H18N2O4SHEPES
5.0 mMC4H10O2S2dithiothreitol
100.0 uMC24H15N3Na2O7S3geranine G

Details: All components outside of protein listed above.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was aggregated at 50 uM protein and 100 uM geranine G dye.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 92000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsImages were low-pass filtered to 16 Angstroms for manual picking.
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.73 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.40 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17652
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 150816 / Details: Manual picking
Startup modelType of model: INSILICO MODEL
In silico model: The model was generated from 2D class averages using the relion_helix_inimodel2d tool.
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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