[English] 日本語
Yorodumi
- EMDB-55930: TAF15 amyloid filament fold B variant 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-55930
TitleTAF15 amyloid filament fold B variant 1
Map dataTAF-15 Type B1 EM map
Sample
  • Tissue: TATA-binding protein-associated factor 2N
    • Protein or peptide: TATA-binding protein-associated factor 2N
  • Ligand: water
KeywordsAmyloid Neurodegeneration Frontotemporal lobar degeneration / PROTEIN FIBRIL
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)
Methodhelical reconstruction / cryo EM / Resolution: 1.64 Å
AuthorsTetter S / Varghese NR / Ryskeldi-Falcon B
Funding support United Kingdom, 1 items
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 3, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_55930.png

Downloads & links

-
Map

FileDownload / File: emd_55930.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTAF-15 Type B1 EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 249.6 Å		0.65 Å/pix.
x 384 pix.
= 249.6 Å		0.65 Å/pix.
x 384 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01115
Minimum - Maximum-0.024260538 - 0.06872634
Average (Standard dev.)0.00008695497 (±0.0023248617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_55930_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: TAF-15 Type B1 half-map 1

Fileemd_55930_half_map_1.map
AnnotationTAF-15 Type B1 half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: TAF-15 Type B1 half-map 2

Fileemd_55930_half_map_2.map
AnnotationTAF-15 Type B1 half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TATA-binding protein-associated factor 2N

EntireName: TATA-binding protein-associated factor 2N
Components
  • Tissue: TATA-binding protein-associated factor 2N
    • Protein or peptide: TATA-binding protein-associated factor 2N
  • Ligand: water

-
Supramolecule #1: TATA-binding protein-associated factor 2N

SupramoleculeName: TATA-binding protein-associated factor 2N / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: TAF15 amyloid filament fold B variant 1
Source (natural)Organism: Homo sapiens (human) / Organ: Brain / Tissue: Prefrontal cortex

-
Macromolecule #1: TATA-binding protein-associated factor 2N

MacromoleculeName: TATA-binding protein-associated factor 2N / type: protein_or_peptide / ID: 1
Details: Each chain is comprised of TAF15 residues 8-93 and 135-145.
Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Prefrontal cortex
Molecular weightTheoretical: 61.909 KDa
SequenceString: MSDSGSYGQS GGEQQSYSTY GNPGSQGYGQ ASQSYSGYGQ TTDSSYGQNY SGYSSYGQSQ SGYSQSYGGY ENQKQSSYSQ QPYNNQGQQ QNMESSGSQG GRAPSYDQPD YGQQDSYDQQ SGYDQHQGSY DEQSNYDQQH DSYSQNQQSY HSQRENYSHH T QDDRRDVS ...String:
MSDSGSYGQS GGEQQSYSTY GNPGSQGYGQ ASQSYSGYGQ TTDSSYGQNY SGYSSYGQSQ SGYSQSYGGY ENQKQSSYSQ QPYNNQGQQ QNMESSGSQG GRAPSYDQPD YGQQDSYDQQ SGYDQHQGSY DEQSNYDQQH DSYSQNQQSY HSQRENYSHH T QDDRRDVS RYGEDNRGYG GSQGGGRGRG GYDKDGRGPM TGSSGGDRGG FKNFGGHRDY GPRTDADSES DNSDNNTIFV QG LGEGVST DQVGEFFKQI GIIKTNKKTG KPMINLYTDK DTGKPKGEAT VSFDDPPSAK AAIDWFDGKE FHGNIIKVSF ATR RPEFMR GGGSGGGRRG RGGYRGRGGF QGRGGDPKSG DWVCPNPSCG NMNFARRNSC NQCNEPRPED SRPSGGDFRG RGYG GERGY RGRGGRGGDR GGYGGDRSGG GYGGDRSSGG GYSGDRSGGG YGGDRSGGGY GGDRGGGYGG DRGGGYGGDR GGGYG GDRG GYGGDRGGGY GGDRGGYGGD RGGYGGDRGG YGGDRGGYGG DRSRGGYGGD RGGGSGYGGD RSGGYGGDRS GGGYGG DRG GGYGGDRGGY GGKMGGRNDY RNDQRNRPY

UniProtKB: TATA-binding protein-associated factor 2N

-
Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 110 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 15741 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.94558 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 1.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 266924
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 850270 / Software - Name: RELION (ver. 5.0.1)
Startup modelType of model: OTHER / Details: De novo initial model helix
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more