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- PDB-5v3h: Crystal structure of SMYD2 with SAM and EPZ033294 -

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Basic information

Entry
Database: PDB / ID: 5v3h
TitleCrystal structure of SMYD2 with SAM and EPZ033294
ComponentsN-lysine methyltransferase SMYD2
KeywordsTRANSFERASE/TRANSFERASE inhibitor / protein-inhibitor complex / protein lysine methyltransferase / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / 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 / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-8WG / DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.69 Å
AuthorsBoriack-Sjodin, P.A.
CitationJournal: Plos One / Year: 2018
Title: Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation.
Authors: Thomenius, M.J. / Totman, J. / Harvey, D. / Mitchell, L.H. / Riera, T.V. / Cosmopoulos, K. / Grassian, A.R. / Klaus, C. / Foley, M. / Admirand, E.A. / Jahic, H. / Majer, C. / Wigle, T. / ...Authors: Thomenius, M.J. / Totman, J. / Harvey, D. / Mitchell, L.H. / Riera, T.V. / Cosmopoulos, K. / Grassian, A.R. / Klaus, C. / Foley, M. / Admirand, E.A. / Jahic, H. / Majer, C. / Wigle, T. / Jacques, S.L. / Gureasko, J. / Brach, D. / Lingaraj, T. / West, K. / Smith, S. / Rioux, N. / Waters, N.J. / Tang, C. / Raimondi, A. / Munchhof, M. / Mills, J.E. / Ribich, S. / Porter Scott, M. / Kuntz, K.W. / Janzen, W.P. / Moyer, M. / Smith, J.J. / Chesworth, R. / Copeland, R.A. / Boriack-Sjodin, P.A.
History
DepositionMar 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: N-lysine methyltransferase SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,90512
Polymers51,0281
Non-polymers1,87711
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.560, 54.775, 79.702
Angle α, β, γ (deg.)90.000, 114.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#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: 51028.379 Da / Num. of mol.: 1
Mutation: N-terminal His tag with TEV cleavage site and FLAG tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD2, KMT3C / Plasmid: pFastBacHTb-lic / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

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Non-polymers , 7 types, 140 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-8WG / N-[1-({1-[(4-chlorophenyl)methyl]-1H-pyrazol-4-yl}methyl)azetidin-3-yl]-1-cyclopropyl-1H-1,2,3-triazole-4-carboxamide


Mass: 411.888 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22ClN7O
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 5% v/v Ethanol, 0.1 M Tris pH 7.5, 26% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.95369 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 17477 / % possible obs: 98.8 % / Redundancy: 3.7 % / Net I/σ(I): 14.6
Reflection shellResolution: 2.69→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 881 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.877 / SU B: 27.126 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.133 / ESU R Free: 0.36
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27 892 5.2 %RANDOM
Rwork0.2175 ---
obs0.2202 16191 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.07 Å2 / Biso mean: 54.016 Å2 / Biso min: 15.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20.16 Å2
2---1.24 Å20 Å2
3---0.82 Å2
Refinement stepCycle: final / Resolution: 2.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 118 129 3768
Biso mean--41.66 36.86 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193748
X-RAY DIFFRACTIONr_bond_other_d0.0020.023536
X-RAY DIFFRACTIONr_angle_refined_deg1.3452.0025047
X-RAY DIFFRACTIONr_angle_other_deg0.9623.0038180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20724.368174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07115670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1421521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02837
LS refinement shellResolution: 2.68→2.749 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 60 -
Rwork0.336 914 -
all-974 -
obs--73.45 %
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)
13.7186-1.8481-1.87791.31931.04126.40010.3290.3820.5406-0.27980.03580.0108-1.5712-0.1444-0.36490.4318-0.02420.00840.16280.21030.2788-39.83241.870917.6891
25.15910.4235-1.32652.34130.68414.6239-0.14540.5086-0.4703-0.26340.0843-0.14460.18690.1330.06110.10680.035-0.00730.1976-0.07640.0735-29.962-18.72717.7733
34.7339-0.6752-2.05547.13490.96831.64380.0393-0.2134-0.6113-0.4108-0.1193-0.76110.08370.68840.080.09880.0996-0.01730.5757-0.02120.2313-15.7712-17.092215.1126
43.3118-0.5046-2.79661.73561.02446.10150.1139-0.31650.16250.21410.1136-0.0998-0.39980.4879-0.22750.1137-0.0061-0.0290.0523-0.03730.04-36.2531-7.540628.3277
51.34551.63071.04966.61290.95221.92630.4582-0.2879-0.48220.3305-0.1107-0.22330.46090.5628-0.34750.70020.2004-0.11740.80050.13250.2793-34.554-22.740548.0261
62.86571.10043.38683.11123.58316.2646-0.0604-0.4881-0.83581.85530.44120.1041.9894-0.0971-0.38082.00870.37750.66480.23310.2060.4858-40.2283-31.173340.2159
72.5006-0.04021.54113.6017-0.43877.6534-0.29960.0229-0.6410.5857-0.00230.61711.0204-0.94040.3020.3872-0.13920.32280.275-0.11060.3554-51.5469-22.68233.8885
82.78123.0210.90638.6468-0.54431.4368-0.31390.0041-0.1712-0.80460.36371.11880.2428-0.828-0.04980.2397-0.17070.04780.8356-0.28080.5386-57.7046-16.644723.2628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 43
2X-RAY DIFFRACTION2A44 - 142
3X-RAY DIFFRACTION3A143 - 182
4X-RAY DIFFRACTION4A183 - 270
5X-RAY DIFFRACTION5A271 - 311
6X-RAY DIFFRACTION6A312 - 355
7X-RAY DIFFRACTION7A356 - 397
8X-RAY DIFFRACTION8A398 - 432

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