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- PDB-7uk1: Complex Structure of Human Polypyrimidine Splicing Factor (PSF/SF... -

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Basic information

Entry
Database: PDB / ID: 7uk1
TitleComplex Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) with Murine Virus-like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of RNA
ComponentsSplicing factor, proline- and glutamine-rich
KeywordsSPLICING / Polypyridimine-binding splicing factor / 5'-polyuridine negative-sense (5'-PUN) template / RNA-dependent DNA-binding regulation / DNA-binding domain (DBD) / RNA-binding motif (RRM) / VL30-1 / Allostery / Cooperativity
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 / 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 / paraspeckles / Suppression of apoptosis / 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 / histone deacetylase binding / nuclear matrix / mRNA processing / 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 / 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 / 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
Splicing factor, proline- and glutamine-rich
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLomakin, I.B. / Wang, J.
Funding support1items
OrganizationGrant numberCountry
Other private
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 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6517
Polymers95,5292
Non-polymers1225
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-73 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.451, 64.658, 68.837
Angle α, β, γ (deg.)90.000, 97.790, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P23246
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 285.15 K / Method: evaporation / pH: 7
Details: 0.1 M MgCl2, 0.1 M HEPES pH 7.0, 15% (w/v),PEG4000, or 15% (w/v) PEG3500, or 20% PEG2000MME

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.69→48.87 Å / Num. obs: 17804 / % possible obs: 98.9 % / Redundancy: 44.1 % / Rpim(I) all: 0.129 / Rrim(I) all: 0.91 / Net I/σ(I): 17.1
Reflection shellResolution: 2.69→2.75 Å / Num. unique obs: 728 / CC1/2: 0.125

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DENZOdata reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wii

4wii


Resolution: 2.7→48.87 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.909 / SU B: 54.257 / SU ML: 0.461 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.291 762 5.2 %RANDOM
Rwork0.2 ---
obs0.2045 13876 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 342.66 Å2 / Biso mean: 112.829 Å2 / Biso min: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å2-0 Å2-0.32 Å2
2---7.2 Å2-0 Å2
3---4.4 Å2
Refinement stepCycle: final / Resolution: 2.7→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 17 16 4085
Biso mean--143.7 112.13 -
Num. residues----501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124159
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6635608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3195503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53221.547265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.24415768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3631543
X-RAY DIFFRACTIONr_chiral_restr0.1230.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023258
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 37 -
Rwork0.376 981 -
all-1018 -
obs--93.48 %
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)
10.785-0.9706-0.32781.21580.58292.22780.1109-0.0299-0.1694-0.1394-0.0030.186-0.0861-0.2882-0.10790.0876-0.0754-0.13190.55750.04990.249-0.6115-28.390411.4872
20.328-0.1003-0.16490.5617-0.19182.1294-0.04540.05350.0862-0.11550.00430.02670.3390.0360.04110.080.0032-0.01480.6171-0.00620.036422.0805-19.14410.9276
30.0719-0.1270.34980.4083-1.20853.8618-0.0727-0.0360.03560.0974-0.1648-0.0439-0.21790.5580.23760.1095-0.0237-0.04870.63080.05540.107741.1606-10.010517.1201
41.7249-0.25681.23692.5372-0.92073.3666-0.1043-0.27590.0219-0.117-0.12460.2116-0.0447-0.25360.22890.0640.0235-0.09030.4933-0.0420.1685-1.731-3.036617.3775
50.3952-0.0767-0.13290.1181-0.21212.191-0.093-0.05710.07150.03840.0116-0.0252-0.0090.04730.08150.10450.0083-0.05660.61420.00040.036220.6084-11.657523.4346
60.3222-0.15011.12870.1817-0.91315.43380.0305-0.0631-0.0033-0.17470.02050.0010.721-0.2922-0.05110.25940.0563-0.00980.62120.04230.010540.6022-20.476621.3452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A286 - 367
2X-RAY DIFFRACTION2A368 - 481
3X-RAY DIFFRACTION3A482 - 601
4X-RAY DIFFRACTION4B286 - 367
5X-RAY DIFFRACTION5B368 - 481
6X-RAY DIFFRACTION6B482 - 601

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