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- PDB-9nzi: NONO homodimer bound to (R)-SKBG-1 -

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Basic information

Entry
Database: PDB / ID: 9nzi
TitleNONO homodimer bound to (R)-SKBG-1
ComponentsNon-POU domain-containing octamer-binding protein
KeywordsRNA BINDING PROTEIN / covalent adduct / splicing factor / DBHS family / paraspeckle
Function / homology
Function and homology information


negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / paraspeckles / lncRNA binding / cellular response to angiotensin / activation of innate immune response / RNA splicing / circadian rhythm / regulation of circadian rhythm / RNA polymerase II transcription regulator complex / nuclear matrix ...negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / paraspeckles / lncRNA binding / cellular response to angiotensin / activation of innate immune response / RNA splicing / circadian rhythm / regulation of circadian rhythm / RNA polymerase II transcription regulator complex / nuclear matrix / fibrillar center / mRNA processing / chromosome / DNA recombination / cellular response to hypoxia / 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 / nucleus / membrane
Similarity search - Function
p54nrb, RNA recognition motif 1 / 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
: / : / Non-POU domain-containing octamer-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsBond, C.S. / Marshall, A.C. / Villa Gomez, A. / Hockley, T.K.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP220103667 Australia
Australian Research Council (ARC)LE230100156 Australia
Australian Research Council (ARC)LE140100096 Australia
CitationJournal: To Be Published
Title: NONO homodimer bound to (R)-SKBG-1
Authors: Bond, C.S. / Marshall, A.C. / Villa Gomez, A. / Hockley, T.K.
History
DepositionMar 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-POU domain-containing octamer-binding protein
B: Non-POU domain-containing octamer-binding protein
C: Non-POU domain-containing octamer-binding protein
D: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8419
Polymers120,8184
Non-polymers2,0235
Water37821
1
A: Non-POU domain-containing octamer-binding protein
B: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4014
Polymers60,4092
Non-polymers9922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-53 kcal/mol
Surface area27020 Å2
MethodPISA
2
C: Non-POU domain-containing octamer-binding protein
D: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4405
Polymers60,4092
Non-polymers1,0313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-47 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.627, 71.141, 101.748
Angle α, β, γ (deg.)90.000, 118.656, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Non-POU domain-containing octamer-binding protein / NonO protein / 54 kDa nuclear RNA- and DNA-binding protein / p54(nrb) / p54nrb / 55 kDa nuclear ...NonO protein / 54 kDa nuclear RNA- and DNA-binding protein / p54(nrb) / p54nrb / 55 kDa nuclear protein / NMT55 / DNA-binding p52/p100 complex / 52 kDa subunit


Mass: 30204.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NONO, NRB54 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: Q15233
#2: Chemical
ChemComp-A1B7J / (2R)-4-(chloroacetyl)-1-(4-methoxybenzene-1-sulfonyl)-N-[(4-methoxyphenyl)methyl]piperazine-2-carboxamide


Mass: 495.976 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H26ClN3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 51.58 % / Description: monoclinic blocks
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Sodium HEPES pH 8 26% (w/v) PEG 2000 MME 1:1 drop:reservoir cryprotected with 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2023
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.52→48.31 Å / Num. obs: 40730 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 75.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Net I/σ(I): 11.6
Reflection shellResolution: 2.52→2.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.046 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3954 / CC1/2: 0.475 / Rpim(I) all: 0.646 / Rrim(I) all: 1.232 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
XDSdata reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→48.31 Å / SU ML: 0.4675 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2681 2129 5.23 %
Rwork0.225 38592 -
obs0.2274 40721 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.5 Å2
Refinement stepCycle: LAST / Resolution: 2.52→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7983 0 112 21 8116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00168252
X-RAY DIFFRACTIONf_angle_d0.398711082
X-RAY DIFFRACTIONf_chiral_restr0.03831151
X-RAY DIFFRACTIONf_plane_restr0.00351471
X-RAY DIFFRACTIONf_dihedral_angle_d14.30283259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.580.41471330.37242457X-RAY DIFFRACTION95.78
2.58-2.650.3761340.31372586X-RAY DIFFRACTION100
2.65-2.720.32291380.31672565X-RAY DIFFRACTION99.89
2.72-2.80.33081240.29782577X-RAY DIFFRACTION99.93
2.8-2.890.41631430.30242590X-RAY DIFFRACTION99.71
2.89-2.990.33571330.32722578X-RAY DIFFRACTION99.93
2.99-3.110.39731590.32872560X-RAY DIFFRACTION99.89
3.11-3.250.3651420.28952590X-RAY DIFFRACTION99.85
3.25-3.430.37361460.27272583X-RAY DIFFRACTION99.78
3.43-3.640.35151020.26492618X-RAY DIFFRACTION99.63
3.64-3.920.27481320.2422564X-RAY DIFFRACTION99.56
3.92-4.310.25771470.19692558X-RAY DIFFRACTION99.12
4.32-4.940.18161290.17762598X-RAY DIFFRACTION98.88
4.94-6.220.24551920.20782556X-RAY DIFFRACTION99.35
6.22-48.310.21921750.16872612X-RAY DIFFRACTION98.03
Refinement TLS params.Method: refined / Origin x: 8.92471788132 Å / Origin y: 26.8151123626 Å / Origin z: 25.3836989629 Å
111213212223313233
T0.628623456092 Å2-0.067908980744 Å2-0.0652130298756 Å2-0.47345775991 Å20.00542051011474 Å2--0.476606889501 Å2
L2.37206383638 °2-0.456338092279 °2-0.69153866582 °2-0.627462323072 °20.136041170744 °2--0.546206919342 °2
S-0.0201438867714 Å °0.033652032362 Å °0.00201202028995 Å °-0.0860709319925 Å °-0.00412156180415 Å °0.122468531331 Å °0.0638646546599 Å °-0.110208153956 Å °0.0311584300583 Å °
Refinement TLS groupSelection details: all

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