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- PDB-7sp0: Crystal structure of human SFPQ L534I mutant in complex with zinc -

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Basic information

Entry
Database: PDB / ID: 7sp0
TitleCrystal structure of human SFPQ L534I mutant in complex with zinc
ComponentsSplicing factor, proline- and glutamine-rich
KeywordsRNA BINDING PROTEIN / SFPQ / DBHS PROTEIN / RRM / ZN / POLYMERIZATION / NUCLEAR PROTEIN / ALS mutation
Function / homology
Function and homology information


PTK6 Regulates Proteins Involved in RNA Processing / negative regulation of circadian rhythm / alternative mRNA splicing, via spliceosome / Suppression of apoptosis / paraspeckles / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of innate immune response / RNA splicing / double-strand break repair via homologous recombination / regulation of circadian rhythm ...PTK6 Regulates Proteins Involved in RNA Processing / negative regulation of circadian rhythm / alternative mRNA splicing, via spliceosome / Suppression of apoptosis / paraspeckles / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of innate immune response / RNA splicing / double-strand break repair via homologous recombination / regulation of circadian rhythm / mRNA processing / nuclear matrix / histone deacetylase binding / RNA polymerase II transcription regulator complex / rhythmic process / transcription cis-regulatory region binding / nuclear speck / chromatin remodeling / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
PSF, RNA recognition motif 1 / PSF, NOPS domain / NOPS / NOPS (NUC059) domain / 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
Splicing factor, proline- and glutamine-rich
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsLee, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Open Biology / Year: 2022
Title: Familial ALS-associated SFPQ variants promote the formation of SFPQ cytoplasmic aggregates in primary neurons.
Authors: Widagdo, J. / Udagedara, S. / Bhembre, N. / Tan, J.Z.A. / Neureiter, L. / Huang, J. / Anggono, V. / Lee, M.
History
DepositionNov 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor, proline- and glutamine-rich
B: Splicing factor, proline- and glutamine-rich
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3194
Polymers60,1882
Non-polymers1312
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-100 kcal/mol
Surface area27640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.607, 62.717, 67.793
Angle α, β, γ (deg.)90.000, 96.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Splicing factor, proline- and glutamine-rich / / 100 kDa DNA-pairing protein / hPOMp100 / DNA-binding p52/p100 complex / 100 kDa subunit / ...100 kDa DNA-pairing protein / hPOMp100 / DNA-binding p52/p100 complex / 100 kDa subunit / Polypyrimidine tract-binding protein-associated-splicing factor / PSF / PTB-associated-splicing factor


Mass: 30094.045 Da / Num. of mol.: 2 / Mutation: L534I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFPQ, PSF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P23246
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% PEG4000, 0.2 M CALCIUM CHLORIDE, 0.1 M MES, PH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.83→45.96 Å / Num. obs: 44977 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.023 / Net I/σ(I): 17.8
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 0.284 / Num. unique obs: 2803 / CC1/2: 0.913 / Rpim(I) all: 0.205 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OWJ

6owj


Resolution: 1.83→45.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.021 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 2280 5.1 %RANDOM
Rwork0.1785 ---
obs0.1805 42676 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.55 Å2 / Biso mean: 34.22 Å2 / Biso min: 16.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å2-0.66 Å2
2---0.01 Å20 Å2
3----1.37 Å2
Refinement stepCycle: final / Resolution: 1.83→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 2 277 4294
Biso mean--24.27 42.15 -
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134157
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173980
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6635602
X-RAY DIFFRACTIONr_angle_other_deg1.3741.5869198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2685512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.83721.515264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36215777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8811543
X-RAY DIFFRACTIONr_chiral_restr0.1950.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02991
LS refinement shellResolution: 1.83→1.878 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 162 -
Rwork0.232 3188 -
all-3350 -
obs--99.82 %

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