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- PDB-7mdn: Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10... -

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Basic information

Entry
Database: PDB / ID: 7mdn
TitleHistone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a
ComponentsHistone-lysine N-methyltransferase NSD2
KeywordsTRANSFERASE / NSD2-PWWP / MRT10241866a / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / regulation of double-strand break repair via nonhomologous end joining / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / membranous septum morphogenesis / atrial septum primum morphogenesis ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / regulation of double-strand break repair via nonhomologous end joining / histone H4K20 methyltransferase activity / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / membranous septum morphogenesis / atrial septum primum morphogenesis / 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 / sequence-specific DNA binding / methylation / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / : / : / : / : / : / : / : / NSD, Cys-His rich domain / 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 superfamily / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-Y6V / Histone-lysine N-methyltransferase NSD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsLei, M. / Freitas, R.F. / Dong, A. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: A chemical probe targeting the PWWP domain alters NSD2 nucleolar localization.
Authors: Dilworth, D. / Hanley, R.P. / Ferreira de Freitas, R. / Allali-Hassani, A. / Zhou, M. / Mehta, N. / Marunde, M.R. / Ackloo, S. / Carvalho Machado, R.A. / Khalili Yazdi, A. / Owens, D.D.G. / ...Authors: Dilworth, D. / Hanley, R.P. / Ferreira de Freitas, R. / Allali-Hassani, A. / Zhou, M. / Mehta, N. / Marunde, M.R. / Ackloo, S. / Carvalho Machado, R.A. / Khalili Yazdi, A. / Owens, D.D.G. / Vu, V. / Nie, D.Y. / Alqazzaz, M. / Marcon, E. / Li, F. / Chau, I. / Bolotokova, A. / Qin, S. / Lei, M. / Liu, Y. / Szewczyk, M.M. / Dong, A. / Kazemzadeh, S. / Abramyan, T. / Popova, I.K. / Hall, N.W. / Meiners, M.J. / Cheek, M.A. / Gibson, E. / Kireev, D. / Greenblatt, J.F. / Keogh, M.C. / Min, J. / Brown, P.J. / Vedadi, M. / Arrowsmith, C.H. / Barsyte-Lovejoy, D. / James, L.I. / Schapira, M.
History
DepositionApr 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)130,70318
Polymers128,0768
Non-polymers2,62710
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-93 kcal/mol
Surface area44150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 69.100, 80.192
Angle α, β, γ (deg.)75.520, 79.360, 60.470
Int Tables number1
Space group name H-MP1

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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: 16009.438 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) / Variant (production host): -V2R-RIL
References: UniProt: O96028, [histone H3]-lysine36 N-dimethyltransferase
#2: Chemical
ChemComp-Y6V / ~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide


Mass: 328.386 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.46 % / Mosaicity: 0.23 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 19, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.42→48.81 Å / Num. obs: 42507 / % possible obs: 90.4 % / Redundancy: 2.1 % / Biso Wilson estimate: 56.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.048 / Rrim(I) all: 0.073 / Net I/σ(I): 8.9 / Num. measured all: 89353
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.1 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.42-2.510.602969645430.7010.5480.8171.591.9
9.05-48.810.01816608060.9990.0170.02528.389.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6XCG

6xcg


Resolution: 2.42→41.42 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.436 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.382 / SU Rfree Blow DPI: 0.253 / SU Rfree Cruickshank DPI: 0.266
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2098 4.94 %RANDOM
Rwork0.217 ---
obs0.218 42500 90.4 %-
Displacement parametersBiso max: 154.3 Å2 / Biso mean: 65.81 Å2 / Biso min: 31.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.3301 Å2-1.2843 Å25.9625 Å2
2--10.9559 Å25.2365 Å2
3----11.2859 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.42→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7473 0 186 14 7673
Biso mean--55.89 41.67 -
Num. residues----1011
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2470SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1324HARMONIC5
X-RAY DIFFRACTIONt_it7889HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion981SEMIHARMONIC5
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_contact8326SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7889HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10736HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion16.22
LS refinement shellResolution: 2.42→2.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2422 40 4.71 %
Rwork0.2312 810 -
all0.2317 850 -
obs--91.77 %
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)
12.7954-0.4339-0.56094.35750.25712.11120.17550.38620.0942-0.5322-0.32040.3045-0.2058-0.28680.1449-0.19640.144-0.1419-0.2183-0.03370.2487-8.75532.202524.1728
22.7395-0.6871-0.35614.5967-0.18471.99930.0144-0.39770.25840.5481-0.0645-0.2953-0.12340.30070.0501-0.2162-0.095-0.0946-0.2035-0.02950.234223.39692.298657.1343
34.0952-0.5070.882.92-0.12023.7041-0.131-0.54170.3930.3894-0.0140.1928-0.3135-0.30740.145-0.22660.04880.0064-0.2839-0.13170.2838-4.41816.161457.3457
43.0043-0.34280.35762.76690.65392.92020.0379-0.4731-0.14820.4203-0.07060.3880.1722-0.29960.0327-0.2479-0.1040.0746-0.21840.01150.2842-8.5998-21.937557.3704
53.5517-0.8319-0.82843.5670.71473.54950.0367-0.4853-0.27010.41370.0064-0.25370.38910.2432-0.0431-0.19590.0187-0.069-0.28490.08890.261719.4262-25.752756.5686
63.75550.4596-0.61462.4843-0.223.4780.08020.4995-0.3256-0.4693-0.14530.29940.3471-0.24360.0651-0.17160.0487-0.1007-0.2863-0.11690.2361-4.6454-25.749123.6366
71.92750.08270.56663.6132-0.69352.97020.15310.4172-0.0454-0.4616-0.1529-0.16270.17060.3898-0.0002-0.19470.13990.0387-0.176-0.02460.255423.3596-21.963424.9144
83.5496-0.27230.53823.24350.85823.33830.09040.56090.3221-0.5689-0.2285-0.2723-0.48340.29660.1381-0.20150.01950.0208-0.30220.12780.260118.88746.099223.5364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A214 - 348
2X-RAY DIFFRACTION2{ B|* }B214 - 348
3X-RAY DIFFRACTION3{ C|* }C217 - 348
4X-RAY DIFFRACTION4{ D|* }D215 - 348
5X-RAY DIFFRACTION5{ E|* }E216 - 348
6X-RAY DIFFRACTION6{ F|* }F217 - 348
7X-RAY DIFFRACTION7{ G|* }G215 - 348
8X-RAY DIFFRACTION8{ H|* }H217 - 348

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