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- PDB-3sde: Crystal structure of a paraspeckle-protein heterodimer, PSPC1/NONO -

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Basic information

Entry
Database: PDB / ID: 3sde
TitleCrystal structure of a paraspeckle-protein heterodimer, PSPC1/NONO
Components
  • Non-POU domain-containing octamer-binding protein
  • Paraspeckle component 1
KeywordsRNA BINDING PROTEIN / RRM / anti parallel right handed coiled-coil / NOPS / DBHS / RNA binding / long non-coding RNA / mRNA / Paraspeckle / Nucleus
Function / homology
Function and homology information


paraspeckles / membraneless organelle assembly / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / activation of innate immune response / RNA splicing / regulation of circadian rhythm / fibrillar center / nuclear matrix / mRNA processing / RNA polymerase II transcription regulator complex ...paraspeckles / membraneless organelle assembly / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / activation of innate immune response / RNA splicing / regulation of circadian rhythm / fibrillar center / nuclear matrix / mRNA processing / RNA polymerase II transcription regulator complex / circadian rhythm / rhythmic process / chromosome / DNA recombination / nuclear speck / innate immune response / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / identical protein binding / membrane / 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 / p54nrb, RNA recognition motif 1 / 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 ...PSP1, RNA recognition motif 1 / PSP1, RNA recognition motif 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1170 / p54nrb, RNA recognition motif 1 / 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
Non-POU domain-containing octamer-binding protein / Paraspeckle component 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsPasson, D.M. / Lee, M. / Bond, C.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body formation.
Authors: Passon, D.M. / Lee, M. / Rackham, O. / Stanley, W.A. / Sadowska, A. / Filipovska, A. / Fox, A.H. / Bond, C.S.
#1: Journal: To be Published
Title: PSPC1/NONO, a paraspeckle-specific heterodimer: from optimisation of C-terminus to diffraction-quality crystals
Authors: Lee, M. / Passon, D.M. / Fox, A.H. / Bond, C.S.
#2: Journal: To be Published
Title: Crystallisation of a paraspeckle protein PSPC1/NONO heterodimer
Authors: Passon, D.M. / Lee, M. / Fox, A.H. / Bond, C.S.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Paraspeckle component 1
B: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,96213
Polymers60,2792
Non-polymers68311
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-36 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.900, 67.180, 94.080
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Paraspeckle component 1 / Paraspeckle protein 1


Mass: 30000.178 Da / Num. of mol.: 1 / Fragment: DBHS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSPC1, PSP1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q8WXF1
#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.: 1 / Fragment: DBHS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NONO, NRB54 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q15233
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3547.59
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop5.528% PEG 3350, 0.5 M NaCl, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop5.518% PEG 3350, 0.5 M NaCl, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97973, 0.97963, 0.95372
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2009
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979731
20.979631
30.953721
ReflectionResolution: 1.9→19.83 Å / Num. all: 43472 / Num. obs: 43472 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 34.98 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 6235 / % possible all: 97.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→19.36 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9271 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2206 5.07 %RANDOM
Rwork0.1832 ---
obs0.1855 43468 --
all-43468 --
Displacement parametersBiso mean: 42.48 Å2
Baniso -1Baniso -2Baniso -3
1--10.5787 Å20 Å24.2396 Å2
2--4.1891 Å20 Å2
3---6.3897 Å2
Refine analyzeLuzzati coordinate error obs: 0.228 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4006 0 44 437 4487
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014133HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055536HARMONIC2
X-RAY DIFFRACTIONt_sintor_deg17.531541SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_d0.0078124HARMONIC2
X-RAY DIFFRACTIONt_plan_d0.0158591HARMONIC5
X-RAY DIFFRACTIONt_bcor_d21.5474133HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion17.52
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2787 157 4.97 %
Rwork0.2357 3004 -
all0.238 3161 -

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