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- PDB-7pu5: Structure of SFPQ-NONO complex -

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Basic information

Entry
Database: PDB / ID: 7pu5
TitleStructure of SFPQ-NONO complex
Components
  • Non-POU domain-containing octamer-binding protein
  • Splicing factor, proline- and glutamine-rich
KeywordsNUCLEAR PROTEIN / DBHS / Paraspeckle / NOPS / RRM
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 / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / lncRNA binding / cellular response to angiotensin / activation of innate immune response ...PTK6 Regulates Proteins Involved in RNA Processing / negative regulation of circadian rhythm / alternative mRNA splicing, via spliceosome / Suppression of apoptosis / paraspeckles / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / lncRNA binding / cellular response to angiotensin / activation of innate immune response / RNA splicing / double-strand break repair via homologous recombination / regulation of circadian rhythm / mRNA processing / fibrillar center / nuclear matrix / circadian rhythm / histone deacetylase binding / RNA polymerase II transcription regulator complex / rhythmic process / chromosome / cellular response to hypoxia / DNA recombination / transcription cis-regulatory region binding / nuclear speck / chromatin remodeling / DNA repair / 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 / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
p54nrb, RNA recognition motif 1 / 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 / Non-POU domain-containing octamer-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.999 Å
AuthorsFribourg, S.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Biochimie / Year: 2022
Title: Crystal structure of SFPQ-NONO heterodimer.
Authors: Schell, B. / Legrand, P. / Fribourg, S.
History
DepositionSep 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: 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: Non-POU domain-containing octamer-binding protein
B: Splicing factor, proline- and glutamine-rich
C: Non-POU domain-containing octamer-binding protein
D: Splicing factor, proline- and glutamine-rich
E: Non-POU domain-containing octamer-binding protein
F: Splicing factor, proline- and glutamine-rich
G: Non-POU domain-containing octamer-binding protein
H: Splicing factor, proline- and glutamine-rich
I: Non-POU domain-containing octamer-binding protein
J: Splicing factor, proline- and glutamine-rich
K: Non-POU domain-containing octamer-binding protein
L: Splicing factor, proline- and glutamine-rich
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,63624
Polymers358,34412
Non-polymers29212
Water0
1
A: Non-POU domain-containing octamer-binding protein
B: Splicing factor, proline- and glutamine-rich
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7734
Polymers59,7242
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Non-POU domain-containing octamer-binding protein
D: Splicing factor, proline- and glutamine-rich
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7734
Polymers59,7242
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Non-POU domain-containing octamer-binding protein
F: Splicing factor, proline- and glutamine-rich
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7734
Polymers59,7242
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Non-POU domain-containing octamer-binding protein
H: Splicing factor, proline- and glutamine-rich
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7734
Polymers59,7242
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Non-POU domain-containing octamer-binding protein
J: Splicing factor, proline- and glutamine-rich
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7734
Polymers59,7242
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Non-POU domain-containing octamer-binding protein
L: Splicing factor, proline- and glutamine-rich
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7734
Polymers59,7242
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)466.999, 66.820, 126.893
Angle α, β, γ (deg.)90.00, 105.89, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Non-POU domain-containing octamer-binding protein / NonO protein / 54 kDa nuclear RNA- and DNA-binding protein / 55 kDa nuclear protein / DNA-binding ...NonO protein / 54 kDa nuclear RNA- and DNA-binding protein / 55 kDa nuclear protein / DNA-binding p52/p100 complex / 52 kDa subunit / NMT55 / p54(nrb) / p54nrb / human NONO


Mass: 30018.410 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NONO, NRB54 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15233
#2: 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 / human SFPQ


Mass: 29705.602 Da / Num. of mol.: 6
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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25 mM Tris-HCl pH8.5, 14-16 % PEG 8K, 20 % w/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.999→48.45 Å / Num. obs: 259406 / % possible obs: 93.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 99.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.069 / Rsym value: 0.148 / Net I/σ(I): 7.2
Reflection shellResolution: 3→3.2 Å / Num. unique obs: 2967 / CC1/2: 0.569 / Rpim(I) all: 0.588

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (16-JUL-2021)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFM

5ifm


Resolution: 2.999→48.45 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.504
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 2903 4.92 %RANDOM
Rwork0.2231 ---
obs0.2246 58969 77.2 %-
Displacement parametersBiso mean: 91.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.0401 Å20 Å2-0.7283 Å2
2---0.003 Å20 Å2
3----0.0372 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.999→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23273 0 12 0 23285
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00823722HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8631860HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8800SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4114HARMONIC5
X-RAY DIFFRACTIONt_it23722HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion18.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2921SEMIHARMONIC5
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_contact17249SEMIHARMONIC4
LS refinement shellResolution: 3→3.1 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3496 -6.1 %
Rwork0.3395 1108 -
all0.3402 1180 -
obs--16.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.48610.27210.94852.5401-0.21522.06510.01890.12080.3875-0.0226-0.06250.4153-0.04-0.14170.0436-0.10160.08670.0945-0.0573-0.1024-0.1078-74.5731-33.764446.6442
22.5271-0.05251.03681.62570.27981.8211-0.04040.07830.3721-0.1108-0.05920.3177-0.1153-0.18560.0997-0.09860.01270.056-0.1096-0.0607-0.1064-56.7319-68.1183-14.9313
32.3809-0.14170.50812.534-0.29491.28540.01190.1876-0.07080.0853-0.1-0.54160.0305-0.24280.0881-0.11780.061-0.0554-0.304-0.0936-0.0803-22.7783-37.821919.4758
43.0523-0.45560.32211.9330.06871.32280.034-0.4341-0.19060.0902-0.02370.38830.10620.2729-0.0103-0.0335-0.02-0.0359-0.3040.0485-0.03294.509-4.409642.5739
52.4334-0.21490.98542.89740.3652.34920.23250.0311-0.05940.14240.0653-0.52530.10580.1834-0.2978-0.1416-0.05630.0281-0.0365-0.046-0.1344-81.8242-97.1835-45.7382
62.09860.20960.98262.5585-0.17352.51330.1268-0.1678-0.0619-0.1190.18630.5320.0627-0.2884-0.3131-0.08530.01590.0080.3040.1056-0.1293-133.7118-95.2648-16.0857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* B|* }
2X-RAY DIFFRACTION2{ C|* D|* }
3X-RAY DIFFRACTION3{ E|* F|* }
4X-RAY DIFFRACTION4{ G|* H|* }
5X-RAY DIFFRACTION5{ I|* J|* }
6X-RAY DIFFRACTION6{ K|* L|* }

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