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- PDB-6g2b: X-ray structure of NSD3-PWWP1 in complex with compound 8 -

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Basic information

Entry
Database: PDB / ID: 6g2b
TitleX-ray structure of NSD3-PWWP1 in complex with compound 8
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 / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / AWS domain / AWS domain ...: / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / 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 superfamily / SET domain / 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
4-(3-methyl-5-phenyl-imidazol-4-yl)pyridine / Histone-lysine N-methyltransferase NSD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.61 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)16,5072
Polymers16,2711
Non-polymers2351
Water2,522140
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 area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.895, 47.439, 64.301
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-EH8 / 4-(3-methyl-5-phenyl-imidazol-4-yl)pyridine


Mass: 235.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.607→38.17 Å / Num. obs: 18102 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Rsym value: 0.046 / Net I/σ(I): 23.9
Reflection shellResolution: 1.607→1.613 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2609 / CC1/2: 0.817 / Rpim(I) all: 0.325 / Rrim(I) all: 0.824 / Rsym value: 0.944 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
BALBESphasing
RefinementResolution: 1.61→38.17 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.094
RfactorNum. reflection% reflectionSelection details
Rfree0.225 882 4.91 %RANDOM
Rwork0.199 ---
obs0.2 17961 99.9 %-
Displacement parametersBiso max: 117.72 Å2 / Biso mean: 30.78 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.3804 Å20 Å20 Å2
2---4.3548 Å20 Å2
3---0.9745 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.61→38.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 18 140 1211
Biso mean--23.11 40.15 -
Num. residues----123
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d392SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes29HARMONIC2
X-RAY DIFFRACTIONt_gen_planes155HARMONIC5
X-RAY DIFFRACTIONt_it1102HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion130SEMIHARMONIC5
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_contact1318SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1102HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1485HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion14.17
LS refinement shellResolution: 1.61→1.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2694 146 5.14 %
Rwork0.247 2696 -
all0.2482 2842 -
obs--99.83 %
Refinement TLS params.Method: refined / Origin x: -8.0299 Å / Origin y: 9.5444 Å / Origin z: -12.8952 Å
111213212223313233
T-0.0635 Å2-0.0193 Å20.0008 Å2--0.078 Å20.0056 Å2---0.0652 Å2
L2.3866 °2-0.7547 °20.5041 °2-2.1776 °20.3657 °2--2.1963 °2
S-0.0544 Å °0.0083 Å °-0.015 Å °0.1137 Å °0.0351 Å °-0.1134 Å °0.0816 Å °-0.0836 Å °0.0193 Å °
Refinement TLS groupSelection details: { A|* }

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