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Yorodumi- PDB-5xsg: Ultrahigh resolution structure of FUS (37-42) SYSGYS determined b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xsg | |||||||||
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Title | Ultrahigh resolution structure of FUS (37-42) SYSGYS determined by MicroED | |||||||||
Components | RNA-binding protein FUS | |||||||||
Keywords | RNA BINDING PROTEIN / cross-coil amyloid fibril / FUS low complexity domain / reversible amyloid fibril / RNA granule assembly | |||||||||
Function / homology | Function and homology information mRNA stabilization / intracellular non-membrane-bounded organelle / positive regulation of double-strand break repair via homologous recombination / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / transcription coregulator activity ...mRNA stabilization / intracellular non-membrane-bounded organelle / positive regulation of double-strand break repair via homologous recombination / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / transcription coregulator activity / protein homooligomerization / amyloid fibril formation / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 0.73 Å | |||||||||
Authors | Luo, F. / Gui, X. / Zhou, H. / Li, D. / Li, X. / Liu, C. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2018 Title: Atomic structures of FUS LC domain segments reveal bases for reversible amyloid fibril formation. Authors: Feng Luo / Xinrui Gui / Heng Zhou / Jinge Gu / Yichen Li / Xiangyu Liu / Minglei Zhao / Dan Li / Xueming Li / Cong Liu / Abstract: Thermostable cross-β structures are characteristic of pathological amyloid fibrils, but these structures cannot explain the reversible nature of fibrils formed by RNA-binding proteins such as fused ...Thermostable cross-β structures are characteristic of pathological amyloid fibrils, but these structures cannot explain the reversible nature of fibrils formed by RNA-binding proteins such as fused in sarcoma (FUS), involved in RNA granule assembly. Here, we find that two tandem (S/G)Y(S/G) motifs of the human FUS low-complexity domain (FUS LC) form reversible fibrils in a temperature- and phosphorylation-dependent manner. We named these motifs reversible amyloid cores, or RAC1 and RAC2, and determined their atomic structures in fibrillar forms, using microelectron and X-ray diffraction techniques. The RAC1 structure features an ordered-coil fibril spine rather than the extended β-strand typical of amyloids. Ser42, a phosphorylation site of FUS, is critical in the maintenance of the ordered-coil structure, which explains how phosphorylation controls fibril formation. The RAC2 structure shows a labile fibril spine with a wet interface. These structures illuminate the mechanism of reversible fibril formation and dynamic assembly of RNA granules. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5xsg.cif.gz | 11.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xsg.ent.gz | 5.7 KB | Display | PDB format |
PDBx/mmJSON format | 5xsg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/5xsg ftp://data.pdbj.org/pub/pdb/validation_reports/xs/5xsg | HTTPS FTP |
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-Related structure data
Related structure data | 5xrrC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 662.648 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 37-42 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35637 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component |
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Buffer solution | pH: 7 | ||||||||||||||||||
Buffer component | Conc.: 1.95 M / Name: ammonium citrate / Formula: (NH4)2C6H6O7 | ||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 35 % / Chamber temperature: 289 K |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Oct 28, 2015 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: DIFFRACTION |
Image recording | Electron dose: 0.008 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
EM diffraction | Camera length: 520 mm |
EM diffraction shell | Resolution: 0.73→0.829 Å / Fourier space coverage: 85 % / Multiplicity: 4 / Num. of structure factors: 1312 / Phase residual: 39.68 ° |
EM diffraction stats | Fourier space coverage: 81.7 % / High resolution: 0.73 Å / Num. of intensities measured: 4021 / Num. of structure factors: 3872 / Phase error: 35.78 ° / Phase residual: 1 ° / Phase error rejection criteria: 0 / Rmerge: 0.218 / Rsym: 0.218 |
-Processing
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EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90.9 ° / ∠γ: 90 ° / A: 18 Å / B: 4.9 Å / C: 18.6 Å / Space group name: P21 / Space group num: 4 | ||||||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 0.73 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: RECIPROCAL | ||||||||||||||||||||||||||||
Refinement | Resolution: 0.73→2 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 35.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.42 Å2 / Biso mean: 9.563 Å2 / Biso min: 2.58 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.73→2 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0 / Total num. of bins used: 3
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