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- PDB-4rxj: crystal structure of WHSC1L1-PWWP2 -

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Basic information

Entry
Database: PDB / ID: 4rxj
Titlecrystal structure of WHSC1L1-PWWP2
ComponentsHistone-lysine N-methyltransferase NSD3
KeywordsTRANSFERASE / structural genomics / Structural Genomics Consortium / SGC
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsQin, S. / Tempel, W. / Dong, A. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Histone and DNA binding ability studies of the NSD subfamily of PWWP domains.
Authors: Zhang, M. / Yang, Y. / Zhou, M. / Dong, A. / Yan, X. / Loppnau, P. / Min, J. / Liu, Y.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _diffrn_source.type / _struct_ref_seq_dif.details
Revision 1.2Sep 20, 2023Group: 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

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase NSD3


Theoretical massNumber of molelcules
Total (without water)13,2249
Polymers13,2241
Non-polymers08
Water54030
1
A: Histone-lysine N-methyltransferase NSD3

A: Histone-lysine N-methyltransferase NSD3


Theoretical massNumber of molelcules
Total (without water)26,44818
Polymers26,4482
Non-polymers016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area3600 Å2
ΔGint-20 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.357, 99.476, 41.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 13224.050 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WHSC1L1, NSD3, DC28 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2
References: UniProt: Q9BZ95, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 3.5
Details: 25% w/v PEG3350, 10% citric acid, pH 3.5, vapor diffusion, temperature 293K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→34.52 Å / Num. obs: 9973 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.1-2.166.90.63335621816100
8.91-34.525.30.0265984515899

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.3.11data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2DAQ

2daq


Resolution: 2.1→34.52 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2526 / WRfactor Rwork: 0.2046 / FOM work R set: 0.7522 / SU B: 12.324 / SU ML: 0.157 / SU R Cruickshank DPI: 0.1989 / SU Rfree: 0.1833 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Arp/warp was used for automatic model rebuilding. Coot was used for interactive model building. PHENIX.molprobity was used for geometry validation.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 474 4.8 %RANDOM
Rwork0.2295 ---
obs0.2315 9378 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.11 Å2 / Biso mean: 44.555 Å2 / Biso min: 25.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å2-0 Å2
2---0.45 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 8 30 900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019922
X-RAY DIFFRACTIONr_bond_other_d0.0010.02817
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.911261
X-RAY DIFFRACTIONr_angle_other_deg0.78831868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0525116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.70323.61747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40615135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.084155
X-RAY DIFFRACTIONr_chiral_restr0.0880.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
X-RAY DIFFRACTIONr_mcbond_it2.0972.731449
X-RAY DIFFRACTIONr_mcbond_other2.092.727448
X-RAY DIFFRACTIONr_mcangle_it3.0234.081564
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 37 -
Rwork0.295 680 -
all-717 -
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)
15.9208-0.5097-1.00634.9070.69464.5234-0.0193-0.42290.41220.03440.2009-0.0317-0.0542-0.2296-0.18160.02960.037-0.04650.0913-0.070.108711.205336.57333.8223
20.46580.58770.68378.857710.35413.0493-0.10160.1261-0.2847-0.00310.1379-0.11990.14050.4196-0.03620.0798-0.00220.02860.1103-0.02880.271722.950362.512352.9218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A950 - 1022
2X-RAY DIFFRACTION2A1023 - 1064

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