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- PDB-6g3t: X-ray structure of NSD3-PWWP1 -

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Basic information

Entry
Database: PDB / ID: 6g3t
TitleX-ray structure of NSD3-PWWP1
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 ...: / : / : / : / : / : / : / 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
Histone-lysine N-methyltransferase NSD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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 26, 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 1.2Jan 17, 2024Group: 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: Histone-lysine N-methyltransferase NSD3
B: Histone-lysine N-methyltransferase NSD3
C: Histone-lysine N-methyltransferase NSD3
D: Histone-lysine N-methyltransferase NSD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6247
Polymers71,9094
Non-polymers7153
Water2,468137
1
A: Histone-lysine N-methyltransferase NSD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2162
Polymers17,9771
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase NSD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2162
Polymers17,9771
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone-lysine N-methyltransferase NSD3


Theoretical massNumber of molelcules
Total (without water)17,9771
Polymers17,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone-lysine N-methyltransferase NSD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2162
Polymers17,9771
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.178, 88.091, 79.988
Angle α, β, γ (deg.)90.000, 89.880, 90.000
Int Tables number4
Space group name H-MP1211

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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: 17977.309 Da / Num. of mol.: 4
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.528→29.61 Å / Num. obs: 21054 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 54.52 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.056 / Rrim(I) all: 0.147 / Net I/σ(I): 13.2
Reflection shellResolution: 2.528→2.571 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 2.342 / Num. unique obs: 3076 / CC1/2: 0.892 / Rpim(I) all: 0.38 / Rrim(I) all: 0.976 / % possible all: 69.5

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3P

6g3p


Resolution: 2.53→29.61 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.805 / SU R Cruickshank DPI: 0.537 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.516 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.305
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1043 4.95 %RANDOM
Rwork0.229 ---
obs0.231 21054 100 %-
Displacement parametersBiso max: 170.52 Å2 / Biso mean: 53.46 Å2 / Biso min: 16.67 Å2
Baniso -1Baniso -2Baniso -3
1-12.1635 Å20 Å2-2.227 Å2
2---22.453 Å20 Å2
3---10.2895 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 2.53→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 45 137 4080
Biso mean--60.76 38.61 -
Num. residues----457
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1448SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes673HARMONIC5
X-RAY DIFFRACTIONt_it4057HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion478SEMIHARMONIC5
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_contact4263SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4057HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg5476HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion18.84
LS refinement shellResolution: 2.53→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3047 138 4.93 %
Rwork0.2318 2659 -
all0.2355 2797 -
obs--100 %
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)
12.8030.39750.1312.23840.45011.8546-0.0171-0.0634-0.0901-0.00250.03680.06080.02260.058-0.0197-0.1180.0021-0.015-0.0821-0.0112-0.0791-1.04121.981-36.0194
23.2579-1.1732-0.6472.48290.44131.88160.03-0.06290.1759-0.0346-0.00920.0748-0.1140.1343-0.0208-0.0988-0.0051-0.0192-0.0787-0.0064-0.1058-23.593713.9322-34.4655
34.91230.3169-0.09110.4792-0.44257.50720.02830.00750.0314-0.0798-0.03420.03730.0574-0.01410.0059-0.31070.102-0.0270.2742-0.0453-0.3312-25.06546.1595-1.4177
43.62650.29090.52160.697-0.66468.51680.03110.0024-0.0970.0193-0.0099-0.0126-0.0164-0.0917-0.0212-0.3182-0.0659-0.03290.2943-0.0493-0.335-2.44228.648211.0882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A266 - 397
2X-RAY DIFFRACTION2{ B|* }B266 - 395
3X-RAY DIFFRACTION3{ C|* }C266 - 392
4X-RAY DIFFRACTION4{ D|* }D266 - 394

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