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- PDB-9tke: TAF15 amyloid filament fold H (Y38C) -

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Basic information

Entry
Database: PDB / ID: 9tke
TitleTAF15 amyloid filament fold H (Y38C)
ComponentsTATA-binding protein-associated factor 2N
KeywordsPROTEIN FIBRIL / Amyloid Neurodegeneration Frontotemporal lobar degeneration
Function / homology
Function and homology information


mRNA stabilization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA splicing ...mRNA stabilization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA splicing / transcription coregulator activity / mRNA 3'-UTR binding / Regulation of TP53 Activity through Phosphorylation / positive regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
TAF15/EWS/TLS family / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...TAF15/EWS/TLS family / Zinc finger domain / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
TATA-binding protein-associated factor 2N
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsTetter, S. / Varghese, N.R. / Ryskeldi-Falcon, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/25 United Kingdom
CitationJournal: bioRxiv / Year: 2026
Title: Distinct TAF15 amyloid filament folds define multiple subtypes of FTLD-TAF15.
Authors: Stephan Tetter / Nikhil R Varghese / Alexey G Murzin / Wouter De Coster / Marleen Van den Broeck / Sigrun Roeber / Jeffrey T Joseph / Kathy Newell / Rudolf Castellani / Sumit Das / Lee-Cyn ...Authors: Stephan Tetter / Nikhil R Varghese / Alexey G Murzin / Wouter De Coster / Marleen Van den Broeck / Sigrun Roeber / Jeffrey T Joseph / Kathy Newell / Rudolf Castellani / Sumit Das / Lee-Cyn Ang / Matthis Synofzik / Jochen Herms / Rosa Rademakers / Bernardino Ghetti / Tammaryn Lashley / Ian R A Mackenzie / Manuela Neumann / Benjamin Ryskeldi-Falcon /
Abstract: Neurodegenerative diseases are characterised by the assembly of a limited number of disease-specific proteins into amyloid filaments, which form intracellular inclusions or extracellular deposits in ...Neurodegenerative diseases are characterised by the assembly of a limited number of disease-specific proteins into amyloid filaments, which form intracellular inclusions or extracellular deposits in the central nervous system (CNS). We previously found that amyloid filaments of TATA-binding protein-associated factor 15 (TAF15) characterise a subtype of frontotemporal lobar degeneration with FET protein-immunoreactive inclusions (FTLD-FET), termed atypical FTLD with ubiquitin-positive inclusions (aFTLD-U), which causes early-onset, rapidly progressive behavioural variant frontotemporal dementia (FTD). However, it was not clear if TAF15 proteinopathy was more widespread in neurodegenerative diseases. Two additional FTLD-FET subtypes have been proposed, neuronal intermediate filament inclusion body disease (NIFID) and basophilic inclusion body disease (BIBD), which have more heterogenous clinical presentations including FTD, motor neuron diseases (MND) and movement disorders. Here, we used electron cryo-microscopy (cryo-EM) to determine a total of 32 amyloid filament structures from the brains of 17 individuals encompassing all three proposed subtypes of FTLD-FET and their diverse clinical presentations. All cases were characterised by TAF15 filaments, in the absence of filaments of the other FET proteins, fused in sarcoma (FUS) and Ewing's sarcoma (EWS). All three aFTLD-U cases had the previously-reported TAF15 fold. Unexpectedly, we found four distinct TAF15 folds among 11 NIFID cases. Eight of these cases shared a common fold, while the remaining three were each distinct. Furthermore, we found distinct TAF15 folds for each of the three BIBD cases. Neuropathological reassessment of the neocortical TAF15 inclusion pathology of these cases distinguished the NIFID cases with the common fold from the others. Thus, TAF15 filament structures form the basis of a new, expanded classification of FTLD-FET subtypes. Moreover, we discovered a TAF15 Y38C variant in the filament fold of one of the individuals with BIBD. The structure is unable to incorporate wild-type TAF15, despite the individual being heterozygous, suggesting that this variant drives TAF15 filament assembly. This study provides structural and genetic evidence that TAF15 amyloid filaments underlie the diverse group of neurodegenerative diseases currently termed FTLD-FET, which we therefore rename FTLD-TAF15.
History
DepositionDec 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TATA-binding protein-associated factor 2N
B: TATA-binding protein-associated factor 2N
C: TATA-binding protein-associated factor 2N
D: TATA-binding protein-associated factor 2N
E: TATA-binding protein-associated factor 2N


Theoretical massNumber of molelcules
Total (without water)309,2455
Polymers309,2455
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 8 - 92 / Label seq-ID: 8 - 92

Dom-IDAuth asym-IDLabel asym-ID
d_1BB
d_2AA
d_3CC
d_4DD
d_5EE

NCS oper:
IDCodeMatrixVector
1given(0.999111859918, 0.0421365799623, -4.23430532892E-7), (-0.0421365799623, 0.999111859918, -6.42079371944E-8), (4.20348964384E-7, 8.19928260595E-8, 1)-3.78036402668, 3.94314136529, 4.78995314906
2given(0.996448997507, 0.0841985472993, -4.65074030993E-7), (-0.0841985472993, 0.996448997507, 8.49612843367E-9), (4.64137913621E-7, 3.06925991358E-8, 1)-7.39123276531, 8.04214800119, 9.57995394878
3given(0.992015987302, 0.126112176003, -3.77075004028E-7), (-0.126112176003, 0.992015987303, 2.81130243427E-8), (3.77609827082E-7, 1.96651796749E-8, 1)-10.8262262846, 12.2896486245, 14.3699630376
4given(0.985820948664, 0.167800647121, -3.65785143479E-7), (-0.167800647122, 0.985820948664, -1.88630295824E-7), (3.28946371446E-7, 2.4733468096E-7, 1)-14.0791306499, 16.6781770183, 19.1599459495

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Components

#1: Protein
TATA-binding protein-associated factor 2N / 68 kDa TATA-binding protein-associated factor / TAF(II)68 / TAFII68 / RNA-binding protein 56


Mass: 61848.969 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: Amyloid filament formed by TAF15. Each chain is comprised of TAF15 residues 8-92. Y38C variant
Source: (natural) Homo sapiens (human) / Organ: Brain / Tissue: Prefrontal cortex / References: UniProt: Q92804
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: TATA-binding protein-associated factor 2N / Type: TISSUE / Details: TAF15 amyloid filament fold H (Y38C) / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organ: Brain / Tissue: Prefrontal cortex
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15290
EM imaging opticsEnergyfilter name: GIF Quantum ER / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1RELION5.0.1particle selection
2PHENIX1.21.2_5419model refinement
13RELION5.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -2.41 ° / Axial rise/subunit: 4.79 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 85300
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12482 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 53.06 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00623280
ELECTRON MICROSCOPYf_angle_d0.53834410
ELECTRON MICROSCOPYf_chiral_restr0.035360
ELECTRON MICROSCOPYf_plane_restr0.0029635
ELECTRON MICROSCOPYf_dihedral_angle_d17.22031180
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBELECTRON MICROSCOPYNCS constraints1.00768820538E-13
ens_1d_3BBELECTRON MICROSCOPYNCS constraints1.43295025997E-13
ens_1d_4BBELECTRON MICROSCOPYNCS constraints1.67884159064E-13
ens_1d_5BBELECTRON MICROSCOPYNCS constraints1.57465730598E-13

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