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- PDB-9ckf: Crystal structure of SMYD2 secondary binding site mutant -

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Basic information

Entry
Database: PDB / ID: 9ckf
TitleCrystal structure of SMYD2 secondary binding site mutant
ComponentsN-lysine methyltransferase SMYD2
KeywordsTRANSFERASE / SMYD2 / mutant / PARP1 / Methyltransferase / SET and MYND-containing protein
Function / homology
Function and homology information


lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / histone H3 methyltransferase activity / RNA polymerase II complex binding ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / histone H3 methyltransferase activity / RNA polymerase II complex binding / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / heart development / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
SMYD2, SET domain / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. ...SMYD2, SET domain / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, Y. / Spellmon, N. / Perry, E. / Brunzelle, J. / Yang, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Biorxiv / Year: 2024
Title: Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding.
Authors: Zhang, Y. / Alshammari, E. / Sobota, J. / Spellmon, N. / Perry, E. / Cao, T. / Mugunamalwaththa, T. / Smith, S. / Brunzelle, J. / Wu, G. / Stemmler, T. / Jin, J. / Li, C. / Yang, Z.
History
DepositionJul 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-lysine methyltransferase SMYD2
B: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,64313
Polymers99,2062
Non-polymers1,43811
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.188, 52.909, 151.903
Angle α, β, γ (deg.)90.000, 134.746, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein N-lysine methyltransferase SMYD2 / HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain- ...HSKM-B / Histone methyltransferase SMYD2 / Lysine N-methyltransferase 3C / SET and MYND domain-containing protein 2


Mass: 49602.891 Da / Num. of mol.: 2 / Mutation: L351A, W356A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Plasmid: pCDF-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, [histone H3]-lysine4 N-trimethyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.11 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 100 mM Tris-HCl 7.5, 5% ethanol, 1 mM PARP1 peptide, 0.6 mM AdoHcy

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→107.9 Å / Num. obs: 27973 / % possible obs: 94 % / Redundancy: 2.8 % / Biso Wilson estimate: 48.27 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.15 / Χ2: 0.87 / Net I/σ(I): 7.3
Reflection shellResolution: 2.5→2.581 Å / Rmerge(I) obs: 1.225 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1400 / CC1/2: 0.229 / Χ2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.5.32data scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→53.94 Å / SU ML: 0.3786 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1152
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1280 4.58 %Random selection
Rwork0.2215 26676 --
obs0.2229 27956 65.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→53.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6883 0 76 125 7084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327108
X-RAY DIFFRACTIONf_angle_d0.67069579
X-RAY DIFFRACTIONf_chiral_restr0.03961019
X-RAY DIFFRACTIONf_plane_restr0.00381236
X-RAY DIFFRACTIONf_dihedral_angle_d13.65492710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.33850.2971680X-RAY DIFFRACTION37.97
2.6-2.720.3514980.30052023X-RAY DIFFRACTION45.09
2.72-2.860.33691140.30292287X-RAY DIFFRACTION51.17
2.86-3.040.34071330.29932595X-RAY DIFFRACTION57.91
3.04-3.280.3311570.28562846X-RAY DIFFRACTION63.79
3.28-3.610.2871170.26253247X-RAY DIFFRACTION71.6
3.61-4.130.22931810.2083783X-RAY DIFFRACTION83.54
4.13-5.20.20731920.18284031X-RAY DIFFRACTION88.77
5.2-53.940.21432030.18614184X-RAY DIFFRACTION89.2
Refinement TLS params.Method: refined / Origin x: -19.0252155019 Å / Origin y: -16.8131172948 Å / Origin z: -14.1484991196 Å
111213212223313233
T0.243871582256 Å2-0.0293172724539 Å2-0.0857599866377 Å2-0.288811915355 Å2-0.0042371296943 Å2--0.241172625501 Å2
L0.327828864737 °2-0.271411882253 °2-0.448742603074 °2-0.976030291824 °20.327506461815 °2--0.830214915717 °2
S0.0246685925658 Å °0.0243784595569 Å °0.0777853179062 Å °-0.204748277635 Å °-0.0158758303218 Å °0.130308415402 Å °-0.057967376249 Å °0.0691472101659 Å °-0.0044882492055 Å °
Refinement TLS groupSelection details: all

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