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- PDB-5wpa: Structure of human SFPQ/PSPC1 heterodimer -

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Basic information

Entry
Database: PDB / ID: 5wpa
TitleStructure of human SFPQ/PSPC1 heterodimer
Components
  • Paraspeckle component 1
  • Splicing factor, proline- and glutamine-rich
KeywordsNUCLEAR PROTEIN / DBHS protein
Function / homology
Function and homology information


PTK6 Regulates Proteins Involved in RNA Processing / non-membrane-bounded organelle assembly / 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 ...PTK6 Regulates Proteins Involved in RNA Processing / non-membrane-bounded organelle assembly / 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 / fibrillar center / 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 / cytoplasm
Similarity search - Function
PSP1, RNA recognition motif 1 / PSP1, RNA recognition motif 2 / 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 ...PSP1, RNA recognition motif 1 / PSP1, RNA recognition motif 2 / 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 / Paraspeckle component 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsLee, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Crystal structure of a SFPQ/PSPC1 heterodimer provides insights into preferential heterodimerization of human DBHS family proteins.
Authors: Huang, J. / Casas Garcia, G.P. / Perugini, M.A. / Fox, A.H. / Bond, C.S. / Lee, M.
History
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 1, 2020Group: 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor, proline- and glutamine-rich
B: Paraspeckle component 1


Theoretical massNumber of molelcules
Total (without water)59,9662
Polymers59,9662
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-50 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.229, 67.841, 92.204
Angle α, β, γ (deg.)90.00, 95.06, 90.00
Int Tables number5
Space group name H-MC121

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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: 29965.916 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 BL21(DE3) (bacteria) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P23246
#2: Protein Paraspeckle component 1 / / Paraspeckle protein 1


Mass: 30000.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSPC1, PSP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q8WXF1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 0.05 M MES, pH 5.5, 0.2 M sodium chloride, 3% aminohexanoic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.29→26.2 Å / Num. obs: 24463 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 51.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.037 / Net I/σ(I): 12.8
Reflection shellResolution: 2.29→2.39 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2534 / CC1/2: 0.954 / Rpim(I) all: 0.27 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3SDE

3sde


Resolution: 2.29→26.19 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.874 / SU R Cruickshank DPI: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.339 / SU Rfree Blow DPI: 0.248 / SU Rfree Cruickshank DPI: 0.253
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1223 5 %RANDOM
Rwork0.219 ---
obs0.221 24453 98.3 %-
Displacement parametersBiso mean: 57.38 Å2
Baniso -1Baniso -2Baniso -3
1--6.017 Å20 Å22.4497 Å2
2---11.538 Å20 Å2
3---17.555 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.29→26.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 0 136 3999
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093945HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055308HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1450SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes119HARMONIC2
X-RAY DIFFRACTIONt_gen_planes568HARMONIC5
X-RAY DIFFRACTIONt_it3945HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion18.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion493SEMIHARMONIC5
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_contact4313SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.299 140 4.81 %
Rwork0.275 2768 -
all0.276 2908 -
obs--96.36 %

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