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- PDB-7uj1: Crystal structure of PSF-RNA complex -

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Basic information

Entry
Database: PDB / ID: 7uj1
TitleCrystal structure of PSF-RNA complex
Components
  • RNA (30-MER)
  • Splicing factor, proline- and glutamine-rich
KeywordsRNA BINDING PROTEIN/RNA / RNA-recognition motif / DNA binding / transcription regulation / polypyrimidine binding / RNA BINDING PROTEIN-RNA complex
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
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
RNA / RNA (> 10) / Splicing factor, proline- and glutamine-rich
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsSachpatzidis, A. / Wang, J. / Konigsberg, W.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Biochemistry / Year: 2022
Title: Insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript-1.
Authors: Wang, J. / Sachpatzidis, A. / Christian, T.D. / Lomakin, I.B. / Garen, A. / Konigsberg, W.H.
History
DepositionMar 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Splicing factor, proline- and glutamine-rich
B: Splicing factor, proline- and glutamine-rich
D: RNA (30-MER)
E: RNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)113,8094
Polymers113,8094
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.738, 186.738, 55.372
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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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: 47764.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFPQ, PSF / Plasmid: pCDF11 / Production host: Escherichia coli (E. coli) / References: UniProt: P23246
#2: RNA chain RNA (30-MER)


Mass: 9140.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 5mM MgCl2, 1mM DTT, 26% SOKALAN CP 42.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→47.67 Å / Num. obs: 27221 / % possible obs: 99.9 % / Redundancy: 4.465 % / Biso Wilson estimate: 126.644 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.161 / Χ2: 0.785 / Net I/σ(I): 7.5 / Num. measured all: 121547 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.5-3.594.192.6920.5620050.1263.092100
3.59-3.694.0012.1450.719620.1862.48499.7
3.69-3.84.6151.5661.0118910.4351.7799.9
3.8-3.914.7031.1831.4118900.5411.33499.9
3.91-4.044.6630.8871.8917730.6911.00199.9
4.04-4.184.6570.7382.2717380.8110.833100
4.18-4.344.6270.5163.2416950.8720.58399.9
4.34-4.524.5560.3464.6716000.9370.391100
4.52-4.724.520.2515.9915670.9680.28599.8
4.72-4.954.4060.1987.3214760.9750.22599.9
4.95-5.224.2440.1768.0313930.9790.20299.9
5.22-5.533.9280.187.2413420.9780.20899.8
5.53-5.924.7190.1519.5812370.9850.17100
5.92-6.394.7210.11411.9811630.9930.129100
6.39-74.7140.09215.0110910.9930.104100
7-7.834.5640.06419.899770.9970.072100
7.83-9.044.3960.04726.268400.9980.05399.8
9.04-11.073.8980.03729.627260.9970.04399.7
11.07-15.654.7020.03335.635540.9990.037100
15.65-47.674.5180.03435.823010.9980.03996.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wii
Resolution: 3.5→47.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.94 / SU B: 31.534 / SU ML: 0.436 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 711 5 %RANDOM
Rwork0.1649 ---
obs0.1687 13483 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 744.89 Å2 / Biso mean: 171.457 Å2 / Biso min: 56.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å2-0.97 Å20 Å2
2---1.95 Å2-0 Å2
3---6.32 Å2
Refinement stepCycle: final / Resolution: 3.5→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 380 0 10 4729
Biso mean---129 -
Num. residues----557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124834
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.6246567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1395533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25421.643280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.0315823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7281545
X-RAY DIFFRACTIONr_chiral_restr0.1460.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023615
LS refinement shellResolution: 3.5→3.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 55 -
Rwork0.381 973 -
all-1028 -
obs--100 %

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