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- PDB-5ifn: Human PSPC1 Homodimer -

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Basic information

Entry
Database: PDB / ID: 5ifn
TitleHuman PSPC1 Homodimer
ComponentsParaspeckle component 1
KeywordsRNA BINDING PROTEIN / DBHS protein RNA binding
Function / homology
Function and homology information


non-membrane-bounded organelle assembly / paraspeckles / activation of innate immune response / regulation of circadian rhythm / fibrillar center / nuclear matrix / rhythmic process / nuclear speck / innate immune response / negative regulation of DNA-templated transcription ...non-membrane-bounded organelle assembly / paraspeckles / activation of innate immune response / regulation of circadian rhythm / fibrillar center / nuclear matrix / rhythmic process / nuclear speck / innate immune response / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
PSP1, RNA recognition motif 1 / PSP1, RNA recognition motif 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1170 / NOPS / NOPS (NUC059) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RRM (RNA recognition motif) domain / Helix non-globular / RNA recognition motif / RNA recognition motif ...PSP1, RNA recognition motif 1 / PSP1, RNA recognition motif 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1170 / NOPS / NOPS (NUC059) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RRM (RNA recognition motif) domain / Helix non-globular / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Special / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Paraspeckle component 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsKnott, G.J. / Passon, D.M. / Bond, C.S.
CitationJournal: To Be Published
Title: Human PSPC1 Homodimer
Authors: Knott, G.J. / Passon, D.M. / Bond, C.S.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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: Paraspeckle component 1
B: Paraspeckle component 1


Theoretical massNumber of molelcules
Total (without water)59,8862
Polymers59,8862
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-54 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.536, 63.493, 67.800
Angle α, β, γ (deg.)90.00, 98.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Paraspeckle component 1 / / Paraspeckle protein 1


Mass: 29943.121 Da / Num. of mol.: 2 / Fragment: UNP residues 61-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSPC1, PSP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXF1

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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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM (D/L) malic acid pH 7.0 28% PEG 3350 100 mM Tris pH 7.0
Temp details: +/- 0.5 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.542 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 3.17→19.41 Å / Num. obs: 8738 / % possible obs: 97.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 62.07 Å2 / Net I/σ(I): 5.7

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SDE

3sde


Resolution: 3.17→19.41 Å / Cor.coef. Fo:Fc: 0.8233 / Cor.coef. Fo:Fc free: 0.7123 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.608
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 413 4.73 %RANDOM
Rwork0.2368 ---
obs0.2393 8738 98.05 %-
Displacement parametersBiso mean: 59.86 Å2
Baniso -1Baniso -2Baniso -3
1-20.7669 Å20 Å22.9385 Å2
2---24.356 Å20 Å2
3---3.5891 Å2
Refine analyzeLuzzati coordinate error obs: 0.653 Å
Refinement stepCycle: LAST / Resolution: 3.17→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4112 0 0 0 4112
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094193HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.135641HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1545SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes604HARMONIC5
X-RAY DIFFRACTIONt_it4193HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion20.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion529SEMIHARMONIC5
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_contact4798SEMIHARMONIC4
LS refinement shellResolution: 3.17→3.54 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2912 114 4.55 %
Rwork0.2566 2390 -
all0.2583 2504 -
obs--98.05 %

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