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- PDB-5ifm: Human NONO (p54nrb) Homodimer -

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Basic information

Entry
Database: PDB / ID: 5ifm
TitleHuman NONO (p54nrb) Homodimer
ComponentsNon-POU domain-containing octamer-binding protein
KeywordsRNA BINDING PROTEIN / DBHS protein RNA binding
Function / homology
Function and homology information


paraspeckles / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / lncRNA binding / cellular response to angiotensin / activation of innate immune response / RNA splicing / regulation of circadian rhythm / fibrillar center / mRNA processing / nuclear matrix ...paraspeckles / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / lncRNA binding / cellular response to angiotensin / activation of innate immune response / RNA splicing / regulation of circadian rhythm / fibrillar center / mRNA processing / nuclear matrix / circadian rhythm / RNA polymerase II transcription regulator complex / chromosome / cellular response to hypoxia / DNA recombination / nuclear speck / DNA repair / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus
Similarity search - Function
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. ...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
: / PROLINE / Non-POU domain-containing octamer-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKnott, G.J. / Bond, C.S.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1048659 Australia
National Health and Medical Research Council (NHMRC, Australia)1050585 Australia
ARCDPDP160102435 Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: A crystallographic study of human NONO (p54(nrb)): overcoming pathological problems with purification, data collection and noncrystallographic symmetry.
Authors: Knott, G.J. / Panjikar, S. / Thorn, A. / Fox, A.H. / Conte, M.R. / Lee, M. / Bond, C.S.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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: 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
E: Non-POU domain-containing octamer-binding protein
F: Non-POU domain-containing octamer-binding protein
G: Non-POU domain-containing octamer-binding protein
H: Non-POU domain-containing octamer-binding protein
I: Non-POU domain-containing octamer-binding protein
J: Non-POU domain-containing octamer-binding protein
K: Non-POU domain-containing octamer-binding protein
L: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)363,65733
Polymers362,45512
Non-polymers1,20221
Water3,495194
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)60,8228
Polymers60,4092
Non-polymers4136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-56 kcal/mol
Surface area26890 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)60,98511
Polymers60,4092
Non-polymers5769
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12030 Å2
ΔGint-68 kcal/mol
Surface area26870 Å2
MethodPISA
3
E: Non-POU domain-containing octamer-binding protein
F: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5165
Polymers60,4092
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-66 kcal/mol
Surface area26580 Å2
MethodPISA
4
G: Non-POU domain-containing octamer-binding protein
H: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4804
Polymers60,4092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-68 kcal/mol
Surface area26820 Å2
MethodPISA
5
I: Non-POU domain-containing octamer-binding protein
J: Non-POU domain-containing octamer-binding protein


Theoretical massNumber of molelcules
Total (without water)60,4092
Polymers60,4092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-58 kcal/mol
Surface area27070 Å2
MethodPISA
6
K: Non-POU domain-containing octamer-binding protein
L: Non-POU domain-containing octamer-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4453
Polymers60,4092
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-71 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.150, 407.177, 68.961
Angle α, β, γ (deg.)90.000, 97.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: 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: 30204.580 Da / Num. of mol.: 12 / Fragment: UNP residues 53-312
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): NONO / Variant (production host): Rosetta2(DE3) / References: UniProt: Q15233

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Non-polymers , 5 types, 215 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M HEPES pH 8.0 and 20% w/v PEG 3350 / Temp details: +/- 0.5 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.826 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: 0.826 Å / Relative weight: 1
ReflectionResolution: 2.6→48.15 Å / Num. obs: 110370 / % possible obs: 98.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.1
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 1.6 / % possible all: 97.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREPphasing
BUSTER-TNT2.10.0refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CA5

5ca5


Resolution: 2.6→48.15 Å / Cor.coef. Fo:Fc: 0.9174 / Cor.coef. Fo:Fc free: 0.8894 / SU R Cruickshank DPI: 0.858 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.647 / SU Rfree Blow DPI: 0.279 / SU Rfree Cruickshank DPI: 0.292
Details: Autoncs restraints TLS restraints AutomaticFormfactorCorrection
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 5520 5 %RANDOM
Rwork0.1974 ---
obs0.1992 110365 98.66 %-
Displacement parametersBiso max: 190.01 Å2 / Biso mean: 65.87 Å2 / Biso min: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1--5.6 Å20 Å23.3769 Å2
2---7.5908 Å20 Å2
3---13.1908 Å2
Refine analyzeLuzzati coordinate error obs: 0.441 Å
Refinement stepCycle: final / Resolution: 2.6→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25029 0 60 194 25283
Biso mean--60.63 37.34 -
Num. residues----3077
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9593SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes775HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3650HARMONIC5
X-RAY DIFFRACTIONt_it25587HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3130SEMIHARMONIC5
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_contact27166SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d25587HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg34326HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion21.09
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2971 391 4.94 %
Rwork0.2707 7519 -
all0.2721 7910 -
obs--98.66 %
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)
11.5768-0.32320.19851.0453-0.2420.8817-0.0376-0.2559-0.0043-0.0440.08530.09350.1443-0.046-0.0477-0.2654-0.0615-0.12-0.3060.042-0.1267-7.8883-31.609837.3454
21.1326-0.00080.99771.001-0.4570.9192-0.021-0.1732-0.0579-0.0821-0.03130.0220.0727-0.20920.0522-0.2671-0.0346-0.0901-0.20970.0021-0.0957-3.7568-20.612234.9369
31.37630.25980.11691.0572-0.00730.49910.0117-0.02130.04760.069-0.0012-0.0241-0.10430.0318-0.0105-0.24530.0232-0.0841-0.30390.0322-0.140328.12715.70044.3647
40.93540.1556-0.06730.8929-0.19590.71150.105-0.0171-0.02390.0366-0.0571-0.1432-0.0694-0.1271-0.0479-0.25790.0089-0.1598-0.25190.0325-0.117132.1691-5.07747.2082
51.2067-0.614-0.40423.45670.35861.2966-0.05710.0338-0.1306-0.51080.03690.1004-0.0348-0.22140.0202-0.2195-0.1081-0.0663-0.42910.0671-0.223123.2209-57.761732.0326
60.8027-0.2942-0.63093.4640.60181.1968-0.14640.2868-0.1683-0.31020.0230.47810.0561-0.08160.1234-0.2514-0.0902-0.0294-0.42050.0355-0.136219.7048-68.544635.2464
71.47070.84920.5312.60450.28151.25090.13670.00510.13540.4064-0.08190.0206-0.0223-0.1232-0.0549-0.2350.05520.0449-0.44970.0722-0.23460.325132.16097.3674
81.88051.12350.9072.6090.13421.076-0.0785-0.16660.283-0.0364-0.05930.3789-0.17430.00220.1377-0.19070.06720.0244-0.4790.0224-0.151956.745342.5273.1345
90.6310.17290.13611.8360.97382.51530.0427-0.0129-0.03770.03590.1737-0.21090.17910.3666-0.2164-0.232-0.03110.1351-0.5094-0.0143-0.126630.713-95.1376.4861
100.36680.92550.97612.71990.4792.79370.19740.2171-0.14710.19540.0785-0.42580.39970.2697-0.2759-0.1929-0.00640.0299-0.4665-0.0051-0.111427.8468-106.12810.4972
110.4470.01770.03531.7870.58522.28260.0126-0.0102-0.06040.02190.0753-0.1797-0.2156-0.0068-0.0879-0.2112-0.02580.0218-0.45850-0.126468.713471.80627.3139
121.2523-0.50490.01811.76840.21111.69280.0455-0.09460.2185-0.0074-0.0355-0.1209-0.40.0584-0.0099-0.0629-0.04210.0505-0.4730.0009-0.101365.405482.290922.1375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A53 - 306
2X-RAY DIFFRACTION2{ B|* }B54 - 312
3X-RAY DIFFRACTION3{ C|* }C53 - 308
4X-RAY DIFFRACTION4{ D|* }D52 - 308
5X-RAY DIFFRACTION5{ E|* }E53 - 308
6X-RAY DIFFRACTION6{ F|* }F54 - 308
7X-RAY DIFFRACTION7{ G|* }G53 - 307
8X-RAY DIFFRACTION8{ H|* }H54 - 310
9X-RAY DIFFRACTION9{ I|* }I53 - 307
10X-RAY DIFFRACTION10{ J|* }J54 - 312
11X-RAY DIFFRACTION11{ K|* }K54 - 312
12X-RAY DIFFRACTION12{ L|* }L53 - 307

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