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- PDB-9kty: Cryo-EM structure of the TIA-1 prion-like domain amyloid fibril, WT -

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Basic information

Entry
Database: PDB / ID: 9kty
TitleCryo-EM structure of the TIA-1 prion-like domain amyloid fibril, WT
ComponentsCytotoxic granule associated RNA binding protein TIA1
KeywordsPROTEIN FIBRIL / Amyloid fibril / Prion-like domain / RNA-binding protein
Function / homology
Function and homology information


protein localization to cytoplasmic stress granule / nuclear stress granule / poly(A) binding / mRNA 3'-UTR AU-rich region binding / regulation of mRNA splicing, via spliceosome / positive regulation of epithelial cell apoptotic process / FGFR2 alternative splicing / negative regulation of cytokine production / regulation of alternative mRNA splicing, via spliceosome / stress granule assembly ...protein localization to cytoplasmic stress granule / nuclear stress granule / poly(A) binding / mRNA 3'-UTR AU-rich region binding / regulation of mRNA splicing, via spliceosome / positive regulation of epithelial cell apoptotic process / FGFR2 alternative splicing / negative regulation of cytokine production / regulation of alternative mRNA splicing, via spliceosome / stress granule assembly / RNA splicing / mRNA 3'-UTR binding / mRNA processing / cytoplasmic stress granule / negative regulation of translation / ribonucleoprotein complex / apoptotic process / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
TIA-1, RNA recognition motif 1 / TIA-1, RNA recognition motif 2 / TIAR, RNA recognition motif 3 / RNA recognition motif domain, eukaryote / RNA recognition motif / 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
Cytotoxic granule associated RNA binding protein TIA1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsInaoka, D. / Miyata, T. / Makino, F. / Ohtani, Y. / Ekari, M. / Kobayashi, R. / Imamura, K. / Sakamoto, E. / Kodama, S.T. / Yoshida, N. ...Inaoka, D. / Miyata, T. / Makino, F. / Ohtani, Y. / Ekari, M. / Kobayashi, R. / Imamura, K. / Sakamoto, E. / Kodama, S.T. / Yoshida, N. / Kato, T. / Namba, K. / Tochio, H. / Sekiyama, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22H05090 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
CitationJournal: To Be Published
Title: TIA-1 PLD amyloid fibril formation is suppressed by the ALS-associated mutation
Authors: Inaoka, D. / Miyata, T. / Makino, F. / Ohtani, Y. / Ekari, M. / Kobayashi, R. / Imamura, K. / Sakamoto, E. / Kodama, S.T. / Yoshida, N. / Kato, T. / Namba, K. / Tochio, H. / Sekiyama, N.
History
DepositionDec 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 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
C: Cytotoxic granule associated RNA binding protein TIA1
B: Cytotoxic granule associated RNA binding protein TIA1
A: Cytotoxic granule associated RNA binding protein TIA1
E: Cytotoxic granule associated RNA binding protein TIA1
D: Cytotoxic granule associated RNA binding protein TIA1
F: Cytotoxic granule associated RNA binding protein TIA1


Theoretical massNumber of molelcules
Total (without water)62,0716
Polymers62,0716
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cytotoxic granule associated RNA binding protein TIA1 / Nucleolysin TIA-1 isoform p40 / RNA-binding protein TIA-1 / T-cell-restricted intracellular antigen- ...Nucleolysin TIA-1 isoform p40 / RNA-binding protein TIA-1 / T-cell-restricted intracellular antigen-1 / TIA-1 / p40-TIA-1


Mass: 10345.128 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31483
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: Amyloid fibril formed by TIA-1 prion-like domain / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 2
Buffer componentConc.: 0.1 % / Name: Trifluoroacetic acid / Formula: CF3COOH
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 5.353 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4650
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEM3.9image acquisition
4CTFFINDCTF correction
7Coot0.9.8.5model fitting
9PHENIX1.19.2-4158-000model refinement
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.37 ° / Axial rise/subunit: 2.38 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 610417
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56747 / Symmetry type: HELICAL

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