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- PDB-7lrq: Crystal structure of human SFPQ/NONO heterodimer, conserved DBHS ... -

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Basic information

Entry
Database: PDB / ID: 7lrq
TitleCrystal structure of human SFPQ/NONO heterodimer, conserved DBHS region
Components
  • Non-POU domain-containing octamer-binding protein
  • Splicing factor, proline- and glutamine-rich
KeywordsRNA BINDING PROTEIN / DBHS Protein / Nuclear Protein / Nucleic Acid Binding / Paraspeckle Formation
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 / fibrillar center / mRNA processing / 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 / molecular replacement / Resolution: 2.3 Å
AuthorsMarshall, A.C. / Bond, C.S. / Mohnen, I.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1147496 Australia
Australian Research Council (ARC) Australia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Paraspeckle subnuclear bodies depend on dynamic heterodimerisation of DBHS RNA-binding proteins via their structured domains.
Authors: Lee, P.W. / Marshall, A.C. / Knott, G.J. / Kobelke, S. / Martelotto, L. / Cho, E. / McMillan, P.J. / Lee, M. / Bond, C.S. / Fox, A.H.
History
DepositionFeb 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 25, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,1607
Polymers59,9822
Non-polymers1775
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-97 kcal/mol
Surface area25240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.128, 66.128, 203.561
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Components on special symmetry positions
IDModelComponents
11B-63-

ARG

21B-522-

HOH

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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: 29834.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFPQ, PSF / Plasmid: pCDF-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / 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: 30147.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NONO, NRB54 / Plasmid: pET-Duet-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q15233
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 22.5% PEG3350, 0.4 M MgCl2, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 4, 2019
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→43.76 Å / Num. obs: 23840 / % possible obs: 100 % / Redundancy: 54.5 % / Biso Wilson estimate: 60.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.028 / Rrim(I) all: 0.215 / Net I/σ(I): 26.1 / Num. measured all: 1299872 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3842.87.1859724522730.5281.0947.2691.499.9
8.91-43.7651.60.0292571549810.0040.029123.199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wii

4wii


Resolution: 2.3→38.04 Å / SU ML: 0.3646 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.4027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2992 1167 4.91 %
Rwork0.2578 22614 -
obs0.2598 23781 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 5 57 3855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163892
X-RAY DIFFRACTIONf_angle_d0.41165253
X-RAY DIFFRACTIONf_chiral_restr0.0381563
X-RAY DIFFRACTIONf_plane_restr0.0034708
X-RAY DIFFRACTIONf_dihedral_angle_d10.79721485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.39531310.35592758X-RAY DIFFRACTION99.79
2.4-2.530.37051330.32262805X-RAY DIFFRACTION99.9
2.53-2.690.41161640.36972722X-RAY DIFFRACTION99.86
2.69-2.90.37631610.33472782X-RAY DIFFRACTION99.73
2.9-3.190.37171430.33722819X-RAY DIFFRACTION99.97
3.19-3.650.32341560.27722823X-RAY DIFFRACTION100
3.65-4.60.28741270.2242874X-RAY DIFFRACTION100
4.6-38.040.23571520.21223031X-RAY DIFFRACTION100
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)
110.1004855155-3.50670678925-5.827958925347.086308767733.371145503557.92201726960.732006339474-0.08865905197780.664330216385-0.341331594643-0.152880250882-0.868802535037-0.7596878927760.155439467136-0.5369839891770.4789901952550.0385242431269-0.01159588581110.4924420803640.1318412144160.515262418748-16.039839435814.810615016515.8455213788
23.568666416140.4179191752630.7807300339665.13850830742.892747660166.82493230481-0.06201128631850.387051188609-0.0014414905601-0.245624659739-0.003953582721330.0151722407736-0.4275390157690.4311747393070.06966830062790.503852508040.0913141570946-0.07188980802380.82327639245-0.0245918595830.328368885011-26.2009845655-9.689010856793.64007257547
33.588590385630.887142386988-0.1789098032863.61026639231-0.4250820453213.53918211430.1528336586750.1024467271770.166144303747-0.0684240638143-0.1384268217640.255781190253-0.202567811404-0.142647570588-0.02442032988440.3746646721590.113620989801-0.01531916771910.4661080354910.05756478258110.406424747611-32.8668644625-12.789027565529.7006375489
45.064519667842.49730653931.882676152410.23324012750.427407713258.53071772658-0.04201655784970.55539402470.225979393649-0.921533528972-0.134761143437-0.823971191665-0.05389891861410.2355604854320.08976827859650.3721923981490.09122664319590.09249788974890.5535684435710.09008135494230.4422579728311.1900181057-4.6203083695220.19845561
510.27511691330.826453431392-3.363544440765.26360541581-0.00293682769589.266516541810.17384637242-0.372408748817-0.2684724297170.470490891930.0490985448842-0.1297441886760.09602627482540.028430035467-0.2011412067590.3770543509650.005222207937260.001677503362640.2877931252250.005656674464050.301073158333-23.0585177168-8.2699457585735.1069551892
60.1900708295460.424485902734-0.8131806365432.091550307761.433083736199.921730243290.0457912149262-0.0578978236575-0.1351985634540.0445695814453-0.0259067301991-0.05410306714250.3544411707890.157482872832-0.05034574707660.4367157271540.204901052541-0.1102446533280.778683473654-0.004426559065870.460200364251-35.8047656474-15.890763079815.0533712888
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 290 through 367 )AA290 - 3671 - 78
22chain 'A' and (resid 368 through 450 )AA368 - 45079 - 161
33chain 'A' and (resid 451 through 528 )AA451 - 528162 - 239
44chain 'B' and (resid 56 through 145 )BB56 - 1451 - 90
55chain 'B' and (resid 146 through 227 )BB146 - 22791 - 172
66chain 'B' and (resid 228 through 308 )BB228 - 308173 - 247

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