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

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Basic information

Entry
Database: PDB / ID: 7lmt
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 / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / atrial septum primum morphogenesis / membranous septum morphogenesis ...atrial septum secundum morphogenesis / [histone H3]-lysine36 N-dimethyltransferase / histone H4K20 methyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K36 dimethyltransferase activity / histone H3K36 trimethyltransferase activity / positive regulation of isotype switching to IgA isotypes / regulation of establishment of protein localization / atrial septum primum morphogenesis / membranous septum 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 / methylation / sequence-specific DNA binding / 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 / 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 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 / 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: 2.27 Å
AuthorsLei, M. / Freitas, R.F. / Dong, A. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Histone-lysine N-methyltransferase NSD2-PWWP1 with compound MRT10241866a
Authors: Lei, M. / Freitas, R.F. / Dong, A. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionFeb 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-90 kcal/mol
Surface area44420 Å2
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
#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

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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, 0.1M 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: 2.26→48.81 Å / Num. obs: 51608 / % possible obs: 89.9 % / Redundancy: 2.1 % / Biso Wilson estimate: 54.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.056 / Rrim(I) all: 0.084 / Net I/σ(I): 8.6 / Num. measured all: 108433
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
2.26-2.330.982839240780.5080.9021.3380.982
9.33-48.810.01815267410.9990.0170.02533.789.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6XCG

6xcg


Resolution: 2.27→43.25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.286 / SU Rfree Blow DPI: 0.225 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2502 4.89 %RANDOM
Rwork0.218 ---
obs0.221 51137 89.3 %-
Displacement parametersBiso max: 167.5 Å2 / Biso mean: 70.67 Å2 / Biso min: 26.87 Å2
Baniso -1Baniso -2Baniso -3
1--6.0607 Å20.2759 Å2-0.299 Å2
2--1.3336 Å21.7942 Å2
3---4.7271 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 2.27→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7478 0 186 14 7678
Biso mean--61.06 34.3 -
Num. residues----1012
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_it7893HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion982SEMIHARMONIC5
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_contact8302SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7893HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10740HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion16.51
LS refinement shellResolution: 2.27→2.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2258 57 5.57 %
Rwork0.2215 966 -
all0.2218 1023 -
obs--61.26 %
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)
12.7211-0.9685-0.44524.80520.23161.50560.20140.39220.0331-0.5677-0.2990.3336-0.147-0.3070.0976-0.180.1603-0.2247-0.2563-0.07080.5778-8.74772.200424.1668
22.5884-0.0578-0.41674.92550.05391.60590.0003-0.42040.14140.5284-0.0759-0.4009-0.11880.30920.0757-0.2868-0.0546-0.1665-0.325-0.04020.490123.39672.298357.1351
34.5873-0.48111.08143.43750.24273.2878-0.0854-0.5510.31480.44260.02340.1276-0.3044-0.36480.062-0.28510.0655-0.0518-0.3744-0.1250.4961-4.41956.159657.3499
42.4773-0.18460.58642.43710.82982.53230.0225-0.4529-0.08820.3998-0.01640.42640.1851-0.3391-0.0061-0.3329-0.0687-0.0015-0.3515-0.03280.5632-8.6009-21.93857.3805
53.9483-1.152-0.76253.24040.70853.43610.0123-0.5445-0.25270.47530.0182-0.11270.37480.1741-0.0305-0.29670.0305-0.1391-0.43080.04740.515819.4334-25.742956.5806
63.8360.8263-0.09152.02650.45953.11880.06970.5169-0.2115-0.4603-0.13360.18560.2677-0.21280.0639-0.20150.0887-0.1432-0.3554-0.10840.463-4.6406-25.756423.635
71.73130.23980.78393.7001-0.64432.62790.18750.4348-0.0001-0.4923-0.1582-0.12810.10720.4357-0.0293-0.22980.1645-0.0521-0.2819-0.06740.589723.3469-21.963924.7752
84.0014-0.21570.28852.65530.71433.02030.08020.56380.297-0.5573-0.1957-0.1833-0.46570.27280.1156-0.28930.0503-0.0859-0.46180.07810.539118.8926.09323.525
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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