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- PDB-6bwz: SYSGYS from low-complexity domain of FUS, residues 37-42 -

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Basic information

Entry
Database: PDB / ID: 6bwz
TitleSYSGYS from low-complexity domain of FUS, residues 37-42
ComponentsSYSGYS peptide from low-complexity domain of FUS
KeywordsPROTEIN FIBRIL / Amyloid / LARKS / Reversible-amyloid / low-complexity
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 / mRNA Splicing - Major Pathway / RNA splicing / 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 / mRNA Splicing - Major Pathway / RNA splicing / 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 / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsHughes, M.P. / Rodriguez, J.A. / Sawaya, M.R. / Cascio, D. / Tamir, G. / 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 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
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 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: SYSGYS peptide from low-complexity domain of FUS


Theoretical massNumber of molelcules
Total (without water)6631
Polymers6631
Non-polymers00
Water181
1
A: SYSGYS peptide from low-complexity domain of FUS

A: SYSGYS peptide from low-complexity domain of FUS

A: SYSGYS peptide from low-complexity domain of FUS

A: SYSGYS peptide from low-complexity domain of FUS

A: SYSGYS peptide from low-complexity domain of FUS

A: SYSGYS peptide from low-complexity domain of FUS

A: SYSGYS peptide from low-complexity domain of FUS

A: SYSGYS peptide from low-complexity domain of FUS

A: SYSGYS peptide from low-complexity domain of FUS

A: SYSGYS peptide from low-complexity domain of FUS


Theoretical massNumber of molelcules
Total (without water)6,62610
Polymers6,62610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation1_585x,y+3,z1
crystal symmetry operation1_595x,y+4,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_665-x+1,y+3/2,-z1
crystal symmetry operation2_675-x+1,y+5/2,-z1
crystal symmetry operation2_685-x+1,y+7/2,-z1
crystal symmetry operation2_695-x+1,y+9/2,-z1
Unit cell
Length a, b, c (Å)17.569, 4.818, 18.283
Angle α, β, γ (deg.)90.000, 91.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide SYSGYS peptide from low-complexity domain of FUS


Mass: 662.648 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide SYSGYS corresponding tosegment 37-42 of FUS
Source: (synth.) Homo sapiens (human) / References: UniProt: P35637*PLUS
#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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis-Tris pH 6.0, 0.2M Magnesium Formate Dihydrate

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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: Apr 3, 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: 1182 / % possible obs: 82 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.179 / Χ2: 1.334 / Net I/σ(I): 6.5 / Num. measured all: 5560
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.1-1.142.20.4681.008128.4
1.14-1.1830.4371.456148.6
1.18-1.243.80.3311.47172.1
1.24-1.34.70.371.169192.8
1.3-1.395.40.3221.122199.3
1.39-1.495.10.2771.124197.9
1.49-1.645.40.2461.532198
1.64-1.885.50.1731.744199.3
1.88-2.374.80.1621.38195.6
2.37-1004.40.1141.079189.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NVH

3nvh


Resolution: 1.1→18.28 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.034 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0473 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.042
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1646 111 9.4 %RANDOM
Rwork0.1415 ---
obs0.1434 1066 82.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 6.96 Å2 / Biso mean: 3.827 Å2 / Biso min: 2.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.02 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.1→18.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47 0 0 1 48
Biso mean---6.58 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0248
X-RAY DIFFRACTIONr_bond_other_d0.0020.0233
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.98864
X-RAY DIFFRACTIONr_angle_other_deg0.874377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.24255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.45202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.346155
X-RAY DIFFRACTIONr_chiral_restr0.0860.25
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0255
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0213
X-RAY DIFFRACTIONr_rigid_bond_restr1.002381
X-RAY DIFFRACTIONr_sphericity_free4.29151
X-RAY DIFFRACTIONr_sphericity_bonded1.931580
LS refinement shellResolution: 1.102→1.131 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 4 -
Rwork0.309 26 -
all-30 -
obs--29.13 %

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