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- PDB-6ue6: PWWP1 domain of NSD2 in complex with MR837 -

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Basic information

Entry
Database: PDB / ID: 6ue6
TitlePWWP1 domain of NSD2 in complex with MR837
ComponentsHistone-lysine N-methyltransferase NSD2
KeywordsTRANSFERASE / methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H3K36 dimethyltransferase activity / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / atrial septum primum morphogenesis / membranous septum morphogenesis / regulation of establishment of protein localization ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H3K36 dimethyltransferase activity / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / atrial septum primum morphogenesis / membranous septum morphogenesis / regulation of establishment of protein localization / histone H3K36 methyltransferase activity / histone H3 methyltransferase activity / Nonhomologous End-Joining (NHEJ) / bone development / G2/M DNA damage checkpoint / PKMTs methylate histone lysines / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / methylation / sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / : ...: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / : / : / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / : / 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. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-Q5D / Histone-lysine N-methyltransferase NSD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, Y. / Tempel, W. / De Freitas, R.F. / Schapira, M. / Brown, P.J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of Small-Molecule Antagonists of the PWWP Domain of NSD2.
Authors: Ferreira de Freitas, R. / Liu, Y. / Szewczyk, M.M. / Mehta, N. / Li, F. / McLeod, D. / Zepeda-Velazquez, C. / Dilworth, D. / Hanley, R.P. / Gibson, E. / Brown, P.J. / Al-Awar, R. / James, L. ...Authors: Ferreira de Freitas, R. / Liu, Y. / Szewczyk, M.M. / Mehta, N. / Li, F. / McLeod, D. / Zepeda-Velazquez, C. / Dilworth, D. / Hanley, R.P. / Gibson, E. / Brown, P.J. / Al-Awar, R. / James, L.I. / Arrowsmith, C.H. / Barsyte-Lovejoy, D. / Min, J. / Vedadi, M. / Schapira, M. / Allali-Hassani, A.
History
DepositionSep 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 11, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase NSD2
B: Histone-lysine N-methyltransferase NSD2
C: Histone-lysine N-methyltransferase NSD2
D: Histone-lysine N-methyltransferase NSD2
E: Histone-lysine N-methyltransferase NSD2
F: Histone-lysine N-methyltransferase NSD2
G: Histone-lysine N-methyltransferase NSD2
H: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,79167
Polymers128,5328
Non-polymers2,25959
Water00
1
A: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,34911
Polymers16,0661
Non-polymers28210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,34913
Polymers16,0661
Non-polymers28212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3497
Polymers16,0661
Non-polymers2826
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3495
Polymers16,0661
Non-polymers2824
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3497
Polymers16,0661
Non-polymers2826
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3496
Polymers16,0661
Non-polymers2825
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,34913
Polymers16,0661
Non-polymers28212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Histone-lysine N-methyltransferase NSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3495
Polymers16,0661
Non-polymers2824
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.21, 70.32, 228.83
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Histone-lysine N-methyltransferase NSD2 / Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / ...Multiple myeloma SET domain-containing protein / MMSET / Nuclear SET domain-containing protein 2 / Protein trithorax-5 / Wolf-Hirschhorn syndrome candidate 1 protein


Mass: 16066.489 Da / Num. of mol.: 8 / Fragment: UNP residues 211-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSD2, KIAA1090, MMSET, TRX5, WHSC1 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V2R-pRARE2
References: UniProt: O96028, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-Q5D / 4-cyano-N-cyclopropyl-N-[(thiophen-2-yl)methyl]benzamide


Mass: 282.360 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H14N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 51 / Source method: obtained synthetically
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→49.33 Å / Num. obs: 44525 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.092 / Net I/σ(I): 14
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
8.98-49.3399.35.20.0439740.9970.04836.9
2.4-2.4997.56.50.99745000.7291.0841.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VC8

5vc8


Resolution: 2.4→45.3 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.393 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.377 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2275 -RANDOM
Rwork0.235 ---
obs0.236 44447 99.7 %-
Displacement parametersBiso mean: 60.96 Å2
Baniso -1Baniso -2Baniso -3
1--8.2111 Å20 Å20 Å2
2---4.1761 Å20 Å2
3---12.3872 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7136 0 211 0 7347
LS refinement shellResolution: 2.4→2.42 Å
RfactorNum. reflection% reflection
Rfree0.2669 37 -
Rwork0.2298 --
obs0.2316 889 89.53 %
Refinement TLS params.

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)
13.97451.61780.17853.85710.55024.20560.01880.1491-0.22670.14910.01180.0135-0.22670.0135-0.0306-0.022-0.01960.0482-0.2404-0.01-0.10737.06969.8367100.587
21.63690.8982-0.03573.4294-0.14733.3529-0.0089-0.4214-0.0016-0.42140.0108-0.0204-0.0016-0.0204-0.0019-0.091-0.03950.009-0.0542-0.0181-0.07333.112845.769484.9594
33.5055-0.4283-0.50863.6731-2.28436.514-0.21140.29680.27070.29680.02640.41290.27070.41290.185-0.06940.01580.0456-0.1592-0.0098-0.091531.543730.6832109.244
45.40191.7356-0.4353.92180.82231.08940.10151.0885-0.2861.0885-0.04240.1873-0.2860.1873-0.05910.3818-0.045-0.0323-0.271-0.0327-0.365434.644953.5787124.205
55.1487-1.4166-1.16554.06441.16242.2589-0.08490.78080.51080.7808-0.1556-0.19660.5108-0.19660.24050.0568-0.20570.0154-0.08340.0312-0.26810.531717.091786.7181
61.7407-0.3921-0.35852.2203-1.15126.99770.05240.13710.0670.1371-0.0892-1.06720.067-1.06720.0368-0.2529-0.14260.03830.0778-0.1123-0.1232-18.865416.61466.0827
73.78832.1027-0.70213.33770.46993.30930.0749-0.15780.0893-0.1578-0.1587-0.14550.0893-0.14550.0838-0.140.0291-0.0301-0.03730.0006-0.08821.913614.211446.7283
83.21271.19481.72672.64291.02224.04240.30960.26360.40110.2636-0.02030.35860.40110.3586-0.2893-0.13630.0312-0.0802-0.1287-0.02270.0121.161415.680567.3419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|217 - A|346 }
2X-RAY DIFFRACTION2{ B|217 - B|346 }
3X-RAY DIFFRACTION3{ C|217 - C|348 }
4X-RAY DIFFRACTION4{ D|218 - D|346 }
5X-RAY DIFFRACTION5{ E|217 - E|346 }
6X-RAY DIFFRACTION6{ F|217 - F|346 }
7X-RAY DIFFRACTION7{ G|217 - G|346 }
8X-RAY DIFFRACTION8{ H|217 - H|346 }

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