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- PDB-6g24: X-ray structure of NSD3-PWWP1 in complex with compound 3 -

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Basic information

Entry
Database: PDB / ID: 6g24
TitleX-ray structure of NSD3-PWWP1 in complex with compound 3
ComponentsHistone-lysine N-methyltransferase NSD3
KeywordsONCOPROTEIN / Inhibitor / PWWP domain
Function / homology
Function and homology information


[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation ...[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / methylation / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / : / : / : / NSD, Cys-His rich domain / : / : / NSD Cys-His rich domain ...: / : / : / : / : / : / NSD, Cys-His rich domain / : / : / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
2-[(~{E})-2-thiophen-2-ylethenyl]benzoic acid / Histone-lysine N-methyltransferase NSD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBoettcher, J. / Muellauer, B.J. / Weiss-Puxbaum, A. / Zoephel, A.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3.
Authors: Bottcher, J. / Dilworth, D. / Reiser, U. / Neumuller, R.A. / Schleicher, M. / Petronczki, M. / Zeeb, M. / Mischerikow, N. / Allali-Hassani, A. / Szewczyk, M.M. / Li, F. / Kennedy, S. / ...Authors: Bottcher, J. / Dilworth, D. / Reiser, U. / Neumuller, R.A. / Schleicher, M. / Petronczki, M. / Zeeb, M. / Mischerikow, N. / Allali-Hassani, A. / Szewczyk, M.M. / Li, F. / Kennedy, S. / Vedadi, M. / Barsyte-Lovejoy, D. / Brown, P.J. / Huber, K.V.M. / Rogers, C.M. / Wells, C.I. / Fedorov, O. / Rumpel, K. / Zoephel, A. / Mayer, M. / Wunberg, T. / Bose, D. / Zahn, S. / Arnhof, H. / Berger, H. / Reiser, C. / Hormann, A. / Krammer, T. / Corcokovic, M. / Sharps, B. / Winkler, S. / Haring, D. / Cockcroft, X.L. / Fuchs, J.E. / Mullauer, B. / Weiss-Puxbaum, A. / Gerstberger, T. / Boehmelt, G. / Vakoc, C.R. / Arrowsmith, C.H. / Pearson, M. / McConnell, D.B.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase NSD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5022
Polymers16,2711
Non-polymers2301
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.213, 46.741, 63.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-lysine N-methyltransferase NSD3 / Nuclear SET domain-containing protein 3 / Protein whistle / WHSC1-like 1 isoform 9 with ...Nuclear SET domain-containing protein 3 / Protein whistle / WHSC1-like 1 isoform 9 with methyltransferase activity to lysine / Wolf-Hirschhorn syndrome candidate 1-like protein 1 / WHSC1-like protein 1


Mass: 16271.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD3, WHSC1L1, DC28 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BZ95, histone-lysine N-methyltransferase
#2: Chemical ChemComp-EH2 / 2-[(~{E})-2-thiophen-2-ylethenyl]benzoic acid


Mass: 230.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.103→28.95 Å / Num. obs: 7983 / % possible obs: 96.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 31.65 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 22.4
Reflection shellResolution: 2.103→2.139 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.57 / % possible all: 74

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.95 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.276 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.188
RfactorNum. reflection% reflectionSelection details
Rfree0.235 411 5.15 %RANDOM
Rwork0.202 ---
obs0.204 7982 96.1 %-
Displacement parametersBiso max: 131.59 Å2 / Biso mean: 36.83 Å2 / Biso min: 13 Å2
Baniso -1Baniso -2Baniso -3
1--0.7138 Å20 Å20 Å2
2---1.9928 Å20 Å2
3---2.7066 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.1→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 16 85 1134
Biso mean--38.61 39.96 -
Num. residues----121
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d383SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes27HARMONIC2
X-RAY DIFFRACTIONt_gen_planes153HARMONIC5
X-RAY DIFFRACTIONt_it1079HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion129SEMIHARMONIC5
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_contact1214SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1079HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1455HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion15.14
LS refinement shellResolution: 2.1→2.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2949 103 4.98 %
Rwork0.2197 1965 -
all0.2233 2068 -
obs--89.46 %
Refinement TLS params.Method: refined / Origin x: -8.5264 Å / Origin y: -8.8642 Å / Origin z: 12.4553 Å
111213212223313233
T-0.1108 Å20.0112 Å20.0107 Å2--0.1423 Å20.0228 Å2---0.0802 Å2
L4.1775 °21.3052 °2-0.3644 °2-4.4033 °21.004 °2--2.1349 °2
S-0.1506 Å °0.0832 Å °-0.0801 Å °-0.0975 Å °0.1775 Å °-0.0772 Å °-0.0509 Å °0.0556 Å °-0.0268 Å °
Refinement TLS groupSelection details: { A|* }

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