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- PDB-7vi5: Electron crystallographic structure of TIA-1 prion-like domain, w... -

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Basic information

Entry
Database: PDB / ID: 7vi5
TitleElectron crystallographic structure of TIA-1 prion-like domain, wild type sequence
ComponentsTIA-1 prion-like domain
KeywordsPROTEIN FIBRIL / ALS / prion / fibril
Function / homology
Function and homology information


protein localization to cytoplasmic stress granule / nuclear stress granule / mRNA 3'-UTR AU-rich region binding / poly(A) 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 / mRNA 3'-UTR AU-rich region binding / poly(A) 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 / cytoplasm / cytosol
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 CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / Resolution: 1.761 Å
AuthorsTakaba, K. / Maki-Yonekura, S. / Sekiyama, N. / Imamura, K. / Kodama, T. / Tochio, H. / Yonekura, K.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19K06584 Japan
Japan Science and TechnologyJPMJCR1762 Japan
Japan Science and TechnologyJPMJMI20G5 Japan
Japan Agency for Medical Research and Development (AMED)JPMXS0421700121 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures.
Authors: Naotaka Sekiyama / Kiyofumi Takaba / Saori Maki-Yonekura / Ken-Ichi Akagi / Yasuko Ohtani / Kayo Imamura / Tsuyoshi Terakawa / Keitaro Yamashita / Daigo Inaoka / Koji Yonekura / Takashi S ...Authors: Naotaka Sekiyama / Kiyofumi Takaba / Saori Maki-Yonekura / Ken-Ichi Akagi / Yasuko Ohtani / Kayo Imamura / Tsuyoshi Terakawa / Keitaro Yamashita / Daigo Inaoka / Koji Yonekura / Takashi S Kodama / Hidehito Tochio /
Abstract: T cell intracellular antigen-1 (TIA-1) plays a central role in stress granule (SG) formation by self-assembly via the prion-like domain (PLD). In the TIA-1 PLD, amino acid mutations associated with ...T cell intracellular antigen-1 (TIA-1) plays a central role in stress granule (SG) formation by self-assembly via the prion-like domain (PLD). In the TIA-1 PLD, amino acid mutations associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) or Welander distal myopathy (WDM), have been identified. However, how these mutations affect PLD self-assembly properties has remained elusive. In this study, we uncovered the implicit pathogenic structures caused by the mutations. NMR analysis indicated that the dynamic structures of the PLD are synergistically determined by the physicochemical properties of amino acids in units of five residues. Molecular dynamics simulations and three-dimensional electron crystallography, together with biochemical assays, revealed that the WDM mutation E384K attenuated the sticky properties, whereas the ALS mutations P362L and A381T enhanced the self-assembly by inducing β-sheet interactions and highly condensed assembly, respectively. These results suggest that the P362L and A381T mutations increase the likelihood of irreversible amyloid fibrillization after phase-separated droplet formation, and this process may lead to pathogenicity.
History
DepositionSep 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TIA-1 prion-like domain


Theoretical massNumber of molelcules
Total (without water)1,1441
Polymers1,1441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.570, 43.570, 9.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein/peptide TIA-1 prion-like domain / RNA-binding protein TIA-1 / T-cell-restricted intracellular antigen-1 / TIA-1 / p40-TIA-1


Mass: 1144.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P31483

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Region 2 peptides (G377-Q386) of TIA-1 prion-like domain, wild-type
Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.2 Mammonium phosphate(NH4)2HPO41
245 %MPDC6H14O21
30.1 MHEPESC8H18N2O4S1
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3

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Data collection

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingAverage exposure time: 1 sec. / Electron dose: 0.02 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k)
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 20
EM diffractionCamera length: 1058 mm / Tilt angle list: -68 to +68, 1 deg./frame
EM diffraction shellResolution: 1.76→18.9 Å / Fourier space coverage: 99.7 % / Multiplicity: 22.4 / Num. of structure factors: 1149 / Phase residual: 33.9 °
EM diffraction statsFourier space coverage: 99.7 % / High resolution: 1.76 Å / Num. of intensities measured: 25738 / Num. of structure factors: 1149 / Phase error rejection criteria: None / Rmerge: 34.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
EM softwareName: PHENIX / Category: model refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 120 ° / A: 43.57 Å / B: 43.57 Å / C: 9.63 Å / Space group name: P65 / Space group num: 170
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VI4

7vi4


Resolution: 1.761→18.866 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3473 114 9.92 %
Rwork0.2772 1035 -
obs0.2839 1149 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 33.34 Å2 / Biso mean: 12.1368 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 1.76→18.87 Å /
LigandSolventTotal
Num. atoms0 0 76
Num. residues--10
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00977
ELECTRON CRYSTALLOGRAPHYf_angle_d1.072103
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0810
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.00513
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d9.93525
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.761-1.82340.2729120.216897100
1.8234-1.89640.5376110.2337111100
1.8964-1.98260.3799110.285598100
1.9826-2.0870.2723120.272794100
2.087-2.21750.369290.326797100
2.2175-2.38840.3265140.2875111100
2.3884-2.62820.461390.2879100100
2.6282-3.00720.3853100.2997104100
3.0072-3.78380.3303110.2888106100
3.7838-18.8660.2532150.284511799

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