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- PDB-6wmz: Crystal structure of human SFPQ/NONO complex -

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Basic information

Entry
Database: PDB / ID: 6wmz
TitleCrystal structure of human SFPQ/NONO complex
Components
  • Non-POU domain-containing octamer-binding protein
  • Splicing factor, proline- and glutamine-rich
KeywordsNUCLEAR PROTEIN / RNA-binding protein / RRM / NOPS / coiled-coil / paraspeckles
Function / homology
Function and homology information


PTK6 Regulates Proteins Involved in RNA Processing / negative regulation of circadian rhythm / alternative mRNA splicing, via spliceosome / paraspeckles / Suppression of apoptosis / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced neuron 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 / negative regulation of circadian rhythm / alternative mRNA splicing, via spliceosome / paraspeckles / Suppression of apoptosis / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced neuron 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 / circadian rhythm / RNA polymerase II transcription regulator complex / rhythmic process / chromosome / DNA recombination / transcription cis-regulatory region binding / nuclear speck / chromatin remodeling / DNA repair / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / identical protein binding / membrane / 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: 2.85 Å
AuthorsLee, M. / Bond, C.S.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)513935 Australia
Australian Research Council (ARC)DE150101243 Australia
CitationJournal: To Be Published
Title: Structure analysis of human SFPQ/NONO complex
Authors: Lee, M. / Bond, C.S.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Splicing factor, proline- and glutamine-rich
B: Non-POU domain-containing octamer-binding protein
C: Splicing factor, proline- and glutamine-rich
D: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1725
Polymers150,0764
Non-polymers961
Water70339
1
A: Splicing factor, proline- and glutamine-rich
B: Non-POU domain-containing octamer-binding protein


Theoretical massNumber of molelcules
Total (without water)75,0382
Polymers75,0382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-48 kcal/mol
Surface area32720 Å2
MethodPISA
2
C: Splicing factor, proline- and glutamine-rich
D: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1343
Polymers75,0382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-63 kcal/mol
Surface area33140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.630, 112.940, 204.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 44759.383 Da / Num. of mol.: 2
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: 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


Mass: 30278.721 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl (pH 8.5), 0.2 M ammonium sulfate, 19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.85→68.21 Å / Num. obs: 36690 / % possible obs: 99.5 % / Redundancy: 4.7 % / CC1/2: 0.996 / Net I/σ(I): 10.2
Reflection shellResolution: 2.85→2.98 Å / Num. unique obs: 4446 / CC1/2: 0.627

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wii

4wii


Resolution: 2.85→63.436 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.881 / SU B: 20.55 / SU ML: 0.374 / Cross valid method: FREE R-VALUE / ESU R Free: 0.417
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2826 1827 4.986 %
Rwork0.2359 --
all0.238 --
obs-36640 99.153 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.105 Å20 Å20 Å2
2--3.299 Å20 Å2
3----2.194 Å2
Refinement stepCycle: LAST / Resolution: 2.85→63.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8914 0 5 39 8958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0139072
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178525
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.66312155
X-RAY DIFFRACTIONr_angle_other_deg1.0521.58319805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73951081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55621.291612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.262151764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.97115107
X-RAY DIFFRACTIONr_chiral_restr0.0430.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022010
X-RAY DIFFRACTIONr_nbd_refined0.1780.21533
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.27529
X-RAY DIFFRACTIONr_nbtor_refined0.1490.24028
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.24633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2165
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1350.234
X-RAY DIFFRACTIONr_nbd_other0.190.2167
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1120.214
X-RAY DIFFRACTIONr_mcbond_it2.8537.3764336
X-RAY DIFFRACTIONr_mcbond_other2.8527.3754335
X-RAY DIFFRACTIONr_mcangle_it4.79411.0615413
X-RAY DIFFRACTIONr_mcangle_other4.79411.0615414
X-RAY DIFFRACTIONr_scbond_it3.0177.9344736
X-RAY DIFFRACTIONr_scbond_other3.0157.9324733
X-RAY DIFFRACTIONr_scangle_it5.25611.6946742
X-RAY DIFFRACTIONr_scangle_other5.25411.6896737
X-RAY DIFFRACTIONr_lrange_it8.20382.0659306
X-RAY DIFFRACTIONr_lrange_other8.19982.0549306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9240.3371270.3332559X-RAY DIFFRACTION99.7401
2.924-3.0040.3651260.3162475X-RAY DIFFRACTION99.8081
3.004-3.0910.3861130.3052418X-RAY DIFFRACTION99.6457
3.091-3.1860.321260.2882366X-RAY DIFFRACTION99.68
3.186-3.290.2971030.2672292X-RAY DIFFRACTION99.7501
3.29-3.4060.3251190.2622192X-RAY DIFFRACTION99.6121
3.406-3.5340.2981290.2562145X-RAY DIFFRACTION99.6058
3.534-3.6780.3041080.2452026X-RAY DIFFRACTION99.6265
3.678-3.8420.265890.2261979X-RAY DIFFRACTION99.5188
3.842-4.0290.2671100.2221871X-RAY DIFFRACTION99.2982
4.029-4.2460.273980.2111804X-RAY DIFFRACTION99.425
4.246-4.5030.263970.2021714X-RAY DIFFRACTION99.3963
4.503-4.8140.224970.1981582X-RAY DIFFRACTION99.1145
4.814-5.1980.258740.2041508X-RAY DIFFRACTION98.9987
5.198-5.6930.24690.2221397X-RAY DIFFRACTION98.8537
5.693-6.3630.337610.2531242X-RAY DIFFRACTION98.4139
6.363-7.3420.3620.2311101X-RAY DIFFRACTION95.799
7.342-8.9810.249510.167935X-RAY DIFFRACTION96.8566
8.981-12.6520.203380.189766X-RAY DIFFRACTION97.6914
12.652-63.4360.337300.344441X-RAY DIFFRACTION94.7686

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