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- PDB-5xrr: Crystal structure of FUS (54-59) SYSSYG -

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Basic information

Entry
Database: PDB / ID: 5xrr
TitleCrystal structure of FUS (54-59) SYSSYG
ComponentsRNA-binding protein FUS
KeywordsRNA BINDING PROTEIN / reversible amyloid / hydrous amyloid fibril spine / low complexity domain / RNA granule assembly
Function / homology
Function and homology information


mRNA stabilization / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / RNA splicing / mRNA Splicing - Major Pathway / molecular condensate scaffold activity / mRNA 3'-UTR binding / transcription coregulator activity ...mRNA stabilization / intracellular non-membrane-bounded organelle / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of double-strand break repair via homologous recombination / RNA splicing / mRNA Splicing - Major Pathway / molecular condensate scaffold activity / 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 / nucleus / metal ion binding / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.503 Å
AuthorsZhao, M. / Gui, X. / Li, D. / 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 9, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-binding protein FUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7282
Polymers6631
Non-polymers651
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30 Å2
ΔGint-8 kcal/mol
Surface area940 Å2
2
A: RNA-binding protein FUS
hetero molecules

A: RNA-binding protein FUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4564
Polymers1,3252
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_585-x,-y+3,z1
Buried area210 Å2
ΔGint-53 kcal/mol
Surface area1740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.240, 30.270, 4.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

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Components

#1: Protein/peptide RNA-binding protein FUS / 75 kDa DNA-pairing protein / Oncogene FUS / Oncogene TLS / POMp75 / Translocated in liposarcoma protein


Mass: 662.648 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 54-59 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35637
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.54 Å3/Da / Density % sol: 20.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.5 M NaCl, 0.1 M imidazole pH 8.0, 0.2 M zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→20.649 Å / Num. obs: 1197 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 7.674 % / Biso Wilson estimate: 7.77 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.422 / Rrim(I) all: 0.453 / Net I/σ(I): 3.37 / Num. measured all: 9186 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.67.3450.8211.521940.7110.88175.8
1.6-1.87.7160.6272.422710.7980.673100
1.8-27.7730.5153.411980.8010.552100
2-2.37.8250.4833.982060.8240.517100
2.3-37.6770.4054.281640.9520.43493.7
3-57.7680.3145.411380.9790.339100
5-87.2940.3324.92170.990.362100
8-1080.3166.730.338100
10-20.6496.6670.2486.1760.9980.27100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementResolution: 1.503→20.649 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 11.97
RfactorNum. reflection% reflection
Rfree0.2407 78 10.01 %
Rwork0.204 --
obs0.2098 779 94.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 35.23 Å2 / Biso mean: 7.804 Å2 / Biso min: 1.16 Å2
Refinement stepCycle: final / Resolution: 1.503→20.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47 0 1 5 53
Biso mean--13.59 17.7 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00748
X-RAY DIFFRACTIONf_angle_d1.1364
X-RAY DIFFRACTIONf_chiral_restr0.0615
X-RAY DIFFRACTIONf_plane_restr0.0058
X-RAY DIFFRACTIONf_dihedral_angle_d7.00525
LS refinement shellResolution: 1.5029→1.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2407 78 -
Rwork0.204 701 -
all-779 -
obs--95 %

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