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- PDB-6g2o: X-ray structure of NSD3-PWWP1 in complex with compound BI-9321 -

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Basic information

Entry
Database: PDB / ID: 6g2o
TitleX-ray structure of NSD3-PWWP1 in complex with compound BI-9321
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 / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleoplasm / metal ion binding / nucleus
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
Chem-EJE / Histone-lysine N-methyltransferase NSD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 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 23, 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

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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)16,6322
Polymers16,2711
Non-polymers3601
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.279, 47.568, 61.113
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-EJE / [4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-phenyl]methanamine


Mass: 360.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21FN4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
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-F / Detector: PIXEL / Date: Aug 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→25.71 Å / Num. obs: 12538 / % possible obs: 92.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1756 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
BALBESphasing
RefinementResolution: 1.81→25.71 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.224 623 5.09 %RANDOM
Rwork0.193 ---
obs0.195 12236 99.9 %-
Displacement parametersBiso max: 120.36 Å2 / Biso mean: 37.45 Å2 / Biso min: 16.82 Å2
Baniso -1Baniso -2Baniso -3
1-5.0836 Å20 Å20 Å2
2--6.8258 Å20 Å2
3----11.9094 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.81→25.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 27 96 1153
Biso mean--29.4 45.22 -
Num. residues----120
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d383SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes180HARMONIC5
X-RAY DIFFRACTIONt_it1089HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion127SEMIHARMONIC5
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_contact1283SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1089HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1472HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion14.33
LS refinement shellResolution: 1.81→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2576 141 4.9 %
Rwork0.2214 2739 -
all0.2231 2880 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: -8.2139 Å / Origin y: 8.9316 Å / Origin z: -11.8621 Å
111213212223313233
T-0.0711 Å2-0.0155 Å20.0037 Å2--0.071 Å2-0.0014 Å2---0.0702 Å2
L2.5976 °2-0.6569 °20.5228 °2-4.4394 °20.7167 °2--1.4814 °2
S-0.0131 Å °-0.0248 Å °0.0072 Å °0.0568 Å °0.0051 Å °0.0194 Å °0.0132 Å °-0.0035 Å °0.008 Å °
Refinement TLS groupSelection details: { A|* }

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