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- PDB-6bxv: SYSSYGQS from low-complexity domain of FUS, residues 54-61 -

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Basic information

Entry
Database: PDB / ID: 6bxv
TitleSYSSYGQS from low-complexity domain of FUS, residues 54-61
ComponentsFUS
KeywordsPROTEIN FIBRIL / Amyloid / LARKS / Reversible-amyloid / low-complexity
Function / homology
Function and homology information


mRNA stabilization / positive regulation of double-strand break repair via homologous recombination / intracellular non-membrane-bounded organelle / 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 / positive regulation of double-strand break repair via homologous recombination / intracellular non-membrane-bounded organelle / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsHughes, M.P. / Rodriguez, J.A. / Sawaya, M.R. / Cascio, D. / Gonen, T. / Eisenberg, D.S.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/Office of the DirectorAG-04812 United States
National Science Foundation (NSF, United States)MCB-0958111 United States
CitationJournal: Science / Year: 2018
Title: Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks.
Authors: Michael P Hughes / Michael R Sawaya / David R Boyer / Lukasz Goldschmidt / Jose A Rodriguez / Duilio Cascio / Lisa Chong / Tamir Gonen / David S Eisenberg /
Abstract: Subcellular membraneless assemblies are a reinvigorated area of study in biology, with spirited scientific discussions on the forces between the low-complexity protein domains within these assemblies. ...Subcellular membraneless assemblies are a reinvigorated area of study in biology, with spirited scientific discussions on the forces between the low-complexity protein domains within these assemblies. To illuminate these forces, we determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked β sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. By computationally threading the human proteome on our kinked structures, we identified hundreds of low-complexity segments potentially capable of forming such interactions. These segments are found in proteins as diverse as RNA binders, nuclear pore proteins, and keratins, which are known to form networks and localize to membraneless assemblies.
History
DepositionDec 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation ..._pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUS


Theoretical massNumber of molelcules
Total (without water)8781
Polymers8781
Non-polymers00
Water18010
1
A: FUS
x 10


Theoretical massNumber of molelcules
Total (without water)8,77910
Polymers8,77910
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation2_536-x,y-2,-z+11
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation2_566-x,y+1,-z+11
crystal symmetry operation2_546-x,y-1,-z+11
crystal symmetry operation2_576-x,y+2,-z+11
Unit cell
Length a, b, c (Å)49.580, 4.785, 21.812
Angle α, β, γ (deg.)90.000, 95.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide FUS


Mass: 877.855 Da / Num. of mol.: 1 / Fragment: residues 54-61 / Source method: obtained synthetically
Details: Synthetic peptide SYSGYS corresponding tosegment 54-61 of FUS
Source: (synth.) Homo sapiens (human) / References: UniProt: P35637*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.47 Å3/Da / Density % sol: 16.15 % / Mosaicity: 1 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.5M ammonium tartrate dibasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→100 Å / Num. obs: 2168 / % possible obs: 90.9 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.046 / Rrim(I) all: 0.147 / Χ2: 2.245 / Net I/σ(I): 6.9 / Num. measured all: 18606
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.1-1.144.20.5141960.7320.2680.5831.89582
1.14-1.185.10.4612250.9120.2160.5111.58590
1.18-1.248.50.4861960.9590.1660.5151.86689.5
1.24-1.310.50.4241960.9720.1290.4441.95990.7
1.3-1.3910.50.4332030.9550.1320.4541.75491.4
1.39-1.4910.30.3072230.9870.0940.3221.88194.1
1.49-1.6410.20.2272370.9870.0690.2372.13894.8
1.64-1.8890.1872070.980.0620.1982.71494.1
1.88-2.379.20.1192530.9930.0390.1263.08295.5
2.37-1008.10.0732320.9910.0240.0773.0686.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→24.68 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.052 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.034
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1477 206 9.5 %RANDOM
Rwork0.1367 ---
obs0.1378 1960 90.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 33.91 Å2 / Biso mean: 8.928 Å2 / Biso min: 6.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20.03 Å2
2---0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.1→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62 0 0 12 74
Biso mean---19.2 -
Num. residues----8
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0263
X-RAY DIFFRACTIONr_bond_other_d0.0160.0245
X-RAY DIFFRACTIONr_angle_refined_deg0.7551.95784
X-RAY DIFFRACTIONr_angle_other_deg1.1383105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.62457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.10923.3333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.808158
X-RAY DIFFRACTIONr_chiral_restr0.0350.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0217
X-RAY DIFFRACTIONr_rigid_bond_restr3.7833108
X-RAY DIFFRACTIONr_sphericity_free21.77854
X-RAY DIFFRACTIONr_sphericity_bonded4.2635115
LS refinement shellResolution: 1.1→1.128 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 15 -
Rwork0.312 121 -
all-136 -
obs--74.32 %

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