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- PDB-5xsg: Ultrahigh resolution structure of FUS (37-42) SYSGYS determined b... -

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Basic information

Entry
Database: PDB / ID: 5xsg
TitleUltrahigh resolution structure of FUS (37-42) SYSGYS determined by MicroED
ComponentsRNA-binding protein FUS
KeywordsRNA 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
TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / 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
RNA-binding protein FUS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 0.73 Å
AuthorsLuo, F. / Gui, X. / Zhou, H. / Li, D. / Li, X. / Liu, C.
Funding support China, 2items
OrganizationGrant numberCountry
the State HighTech Development Plan the 863 Program2015AA020907 China
the Major State Basic Research Development Program2016YFA0501902 China
CitationJournal: 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
DepositionJun 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: RNA-binding protein FUS


Theoretical massNumber of molelcules
Total (without water)6631
Polymers6631
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area870 Å2
Unit cell
Length a, b, c (Å)18.000, 4.900, 18.600
Angle α, β, γ (deg.)90.000, 90.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide RNA-binding protein FUS / / SER-TYR-SER-GLY-TYR-SER


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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1FUS TR1 in fibrillar formCOMPLEX#10MULTIPLE SOURCES
2FUS TR1 in fibrillar formCOMPLEX#11MULTIPLE SOURCES
Buffer solutionpH: 7
Buffer componentConc.: 1.95 M / Name: ammonium citrate / Formula: (NH4)2C6H6O7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 35 % / Chamber temperature: 289 K

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Oct 28, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 0.008 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
EM diffractionCamera length: 520 mm
EM diffraction shellResolution: 0.73→0.829 Å / Fourier space coverage: 85 % / Multiplicity: 4 / Num. of structure factors: 1312 / Phase residual: 39.68 °
EM diffraction statsFourier 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

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
EM software
IDNameVersionCategory
6Coot0.8.7model fitting
13PHENIX1.1model refinement
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 correctionType: NONE
3D reconstructionResolution: 0.73 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: BACKBONE TRACE / Space: RECIPROCAL
RefinementResolution: 0.73→2 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 35.94
RfactorNum. reflection% reflection
Rfree0.2886 393 10.15 %
Rwork0.2605 --
obs0.2633 3872 83.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.42 Å2 / Biso mean: 9.563 Å2 / Biso min: 2.58 Å2
Refinement stepCycle: final / Resolution: 0.73→2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47 0 0 1 48
Biso mean---3.87 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.01448
ELECTRON CRYSTALLOGRAPHYf_angle_d1.26564
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.1165
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0068
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d9.2215
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.73-0.8290.38861340.34571178131285
0.829-1.02080.34981270.30051159128685
1.0208-1.99980.25061320.23221142127481

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