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- PDB-6g3p: X-ray structure of seleno-methionine labelled NSD3-PWWP1 -

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Basic information

Entry
Database: PDB / ID: 6g3p
TitleX-ray structure of seleno-methionine labelled 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 / 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 / SAD / MAD / Resolution: 2.8 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

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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


Theoretical massNumber of molelcules
Total (without water)72,2844
Polymers72,2844
Non-polymers00
Water95553
1
A: Histone-lysine N-methyltransferase NSD3


Theoretical massNumber of molelcules
Total (without water)18,0711
Polymers18,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase NSD3


Theoretical massNumber of molelcules
Total (without water)18,0711
Polymers18,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone-lysine N-methyltransferase NSD3


Theoretical massNumber of molelcules
Total (without water)18,0711
Polymers18,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone-lysine N-methyltransferase NSD3


Theoretical massNumber of molelcules
Total (without water)18,0711
Polymers18,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.040, 88.550, 77.970
Angle α, β, γ (deg.)90.000, 90.080, 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 / NSD3-PWWP1


Mass: 18071.100 Da / Num. of mol.: 4 / Fragment: UNP residues 247-398
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.5 Å3/Da / Density % sol: 50.81 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 50 mM TRIS pH 9.0, 23% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→17.28 Å / Num. obs: 29364 / % possible obs: 99.2 % / Redundancy: 3.509 % / Biso Wilson estimate: 48.55 Å2 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.183 / Χ2: 0.875 / Net I/σ(I): 7.79
Reflection shellResolution: 2.8→3 Å / Redundancy: 3.526 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5430 / Rrim(I) all: 0.548 / % possible all: 97.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.8→17.28 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.805 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.366
RfactorNum. reflection% reflectionSelection details
Rfree0.262 792 5.28 %RANDOM
Rwork0.219 ---
obs0.221 14989 99.4 %-
Displacement parametersBiso max: 127.71 Å2 / Biso mean: 34.27 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-6.6292 Å20 Å20.887 Å2
2---10.2531 Å20 Å2
3---3.6239 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.8→17.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 0 53 4067
Biso mean---19.27 -
Num. residues----473
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1464SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes691HARMONIC5
X-RAY DIFFRACTIONt_it4127HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
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_contact4302SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4127HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg5568HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion18.74
LS refinement shellResolution: 2.8→2.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2309 131 4.86 %
Rwork0.2152 2564 -
all0.2161 2695 -
obs--98.54 %
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)
12.20530.46110.08570.45460.31140.31730.04880.0395-0.0883-0.00990.01170.0267-0.02610.118-0.0605-0.03010.0010.0063-0.0816-0.0086-0.0371-1.9862.5008-33.7412
22.4965-0.62080.41031.9752-0.00540.41170.0112-0.10150.1566-0.05510.0293-0.0121-0.08840.0623-0.0405-0.03680.0026-0.0038-0.1124-0.0335-0.0618-24.839814.8723-34.4424
33.0865-0.86380.71280.2901-1.05274.7749-0.0044-0.0006-0.0929-0.02560.0078-0.0249-0.00410.0686-0.0034-0.13670.0109-0.00140.113-0.0371-0.246-25.68985.8507-1.2469
42.5570.6285-1.28731.46-1.22935.74680.0126-0.01580.0231-0.0443-0.01220.007-0.00780.0307-0.0004-0.0915-0.0555-0.01040.0078-0.0303-0.2314-3.11949.465111.4501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A249 - 395
2X-RAY DIFFRACTION2{ B|* }B266 - 395
3X-RAY DIFFRACTION3{ C|* }C266 - 390
4X-RAY DIFFRACTION4{ D|* }D266 - 390

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