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- PDB-9axz: geranine G-induced 2N4R tau filaments -

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Basic information

Entry
Database: PDB / ID: 9axz
Titlegeranine G-induced 2N4R tau filaments
ComponentsIsoform Tau-F of Microtubule-associated protein tau
KeywordsPROTEIN FIBRIL / microtubule / amyloid / tauopathy
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMalyshka, D. / Kuret, J.
Funding support United States, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform Tau-F of Microtubule-associated protein tau
B: Isoform Tau-F of Microtubule-associated protein tau
C: Isoform Tau-F of Microtubule-associated protein tau
D: Isoform Tau-F of Microtubule-associated protein tau
E: Isoform Tau-F of Microtubule-associated protein tau
F: Isoform Tau-F of Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,1869
Polymers275,5196
Non-polymers1,6673
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Isoform Tau-F of Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 45919.871 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPT, MAPTL, MTBT1, TAU / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RP / References: UniProt: P10636-8
#2: Chemical ChemComp-A1AHG / 4-hydroxy-3-{(E)-[4-(6-methyl-1,3-benzothiazol-2-yl)phenyl]diazenyl}naphthalene-2,7-disulfonic acid


Mass: 555.603 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H17N3O7S3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: 2N4R tau in complex with geranine G dye, its inducer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 96.4 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 RP
Buffer solutionpH: 7.4 / Details: All components outside of protein listed above.
Buffer component
IDConc.NameFormulaBuffer-ID
1125 mMsodium chlorideNaCl1
210 mMHEPESC8H18N2O4S1
35 mMdithiothreitolC4H10O2S21
4100 uMgeranine GC24H15N3Na2O7S31
SpecimenConc.: 2.29 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample was aggregated at 50 uM protein and 100 uM geranine G dye.
Specimen supportDetails: 20 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
Image processingDetails: Images were low-pass filtered to 16 Angstroms for manual picking.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -1.4 ° / Axial rise/subunit: 4.73 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 150816 / Details: Manual picking
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17652 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032799
ELECTRON MICROSCOPYf_angle_d0.6573783
ELECTRON MICROSCOPYf_dihedral_angle_d6.828353
ELECTRON MICROSCOPYf_chiral_restr0.062420
ELECTRON MICROSCOPYf_plane_restr0.005453

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