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- PDB-6ncq: The dimerization domain of human SFPQ in space group C2221 -

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Basic information

Entry
Database: PDB / ID: 6ncq
TitleThe dimerization domain of human SFPQ in space group C2221
ComponentsSplicing factor, proline- and glutamine-rich
KeywordsNUCLEAR PROTEIN / DBHS protein RNA binding protein Gene regulation
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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1170 / PSF, RNA recognition motif 1 / PSF, NOPS domain / NOPS / NOPS (NUC059) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RRM (RNA recognition motif) domain / Helix non-globular / RNA recognition motif / RNA recognition motif ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1170 / PSF, RNA recognition motif 1 / PSF, NOPS domain / NOPS / NOPS (NUC059) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RRM (RNA recognition motif) domain / Helix non-globular / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Special / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Splicing factor, proline- and glutamine-rich
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLee, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE150101243 Australia
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: A new crystal structure and small-angle X-ray scattering analysis of the homodimer of human SFPQ.
Authors: Hewage, T.W. / Caria, S. / Lee, M.
History
DepositionDec 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,0941
Polymers30,0941
Non-polymers00
Water3,747208
1
A: Splicing factor, proline- and glutamine-rich

A: Splicing factor, proline- and glutamine-rich


Theoretical massNumber of molelcules
Total (without water)60,1882
Polymers60,1882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area9040 Å2
ΔGint-52 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.131, 119.167, 72.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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 / PTB-associated-splicing factor


Mass: 30094.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFPQ, PSF / Production host: Escherichia coli (E. coli) / References: UniProt: P23246
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl (pH 8,5), 35-40% (v/v) MPD

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→20.49 Å / Num. obs: 22646 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 30.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.1 % / Num. unique obs: 1436 / CC1/2: 0.827 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wii

4wii


Resolution: 1.9→20.49 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.17 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1113 4.91 %RANDOM
Rwork0.201 ---
obs0.204 22646 99.8 %-
Displacement parametersBiso mean: 37.33 Å2
Baniso -1Baniso -2Baniso -3
1--13.1541 Å20 Å20 Å2
2--3.7083 Å20 Å2
3---9.4458 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.9→20.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 0 208 2262
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012155HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.982909HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d809SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes384HARMONIC5
X-RAY DIFFRACTIONt_it2155HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion16.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion269SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2583SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.91 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.323 -6.84 %
Rwork0.2483 422 -
all0.2529 453 -
obs--99.77 %

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