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- PDB-5v37: Crystal structure of SMYD3 with SAM and EPZ028862 -

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Basic information

Entry
Database: PDB / ID: 5v37
TitleCrystal structure of SMYD3 with SAM and EPZ028862
ComponentsHistone-lysine N-methyltransferase SMYD3
KeywordsTRANSFERASE/TRANSFERASE inhibitor / protein-inhibitor complex / protein lysine methyltransferase / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines ...histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines / nucleosome assembly / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type ...Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Annexin V; domain 1 / Tetratricopeptide repeat domain / Helix Hairpins / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / Helix non-globular / Beta Complex / Special / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-8WD / DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.42 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 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 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 1.2Mar 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: Histone-lysine N-methyltransferase SMYD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,61612
Polymers49,1501
Non-polymers1,46611
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.818, 65.868, 107.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone-lysine N-methyltransferase SMYD3 / SET and MYND domain-containing protein 3 / Zinc finger MYND domain-containing protein 1


Mass: 49150.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Plasmid: pET21W7-Sumo / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H7B4, histone-lysine N-methyltransferase

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Non-polymers , 7 types, 509 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-8WD / N-{(3-endo)-8-[(trans-4-aminocyclohexyl)sulfonyl]-8-azabicyclo[3.2.1]octan-3-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide


Mass: 422.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N4O4S
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.10 M Magnesium formate, 0.1M Tris 8.0, 14% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→17.26 Å / Num. obs: 75322 / % possible obs: 97.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.8
Reflection shellResolution: 1.42→1.45 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.6 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
KYLINdata reduction
KYLINdata scaling
RefinementResolution: 1.42→17.26 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.125 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.097
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2789 3831 4.8 %RANDOM
Rwork0.2276 ---
obs0.23 75322 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.8 Å2 / Biso mean: 18.09 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å2-0 Å20 Å2
2--1.11 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 1.42→17.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 87 499 3981
Biso mean--18 26.99 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193875
X-RAY DIFFRACTIONr_bond_other_d0.0020.023775
X-RAY DIFFRACTIONr_angle_refined_deg1.3592.0035236
X-RAY DIFFRACTIONr_angle_other_deg0.9343.0038721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52223.771175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95815735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9431533
X-RAY DIFFRACTIONr_chiral_restr0.0770.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214341
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02871
X-RAY DIFFRACTIONr_rigid_bond_restr4.71337650
X-RAY DIFFRACTIONr_sphericity_free26.835207
X-RAY DIFFRACTIONr_sphericity_bonded9.86757843
LS refinement shellResolution: 1.424→1.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 230 -
Rwork0.478 4956 -
all-5186 -
obs--87.9 %

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