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- PDB-6yuh: Crystal structure of SMYD3 with diperodon R enantiomer bound to a... -

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Basic information

Entry
Database: PDB / ID: 6yuh
TitleCrystal structure of SMYD3 with diperodon R enantiomer bound to allosteric site
ComponentsHistone-lysine N-methyltransferase SMYD3
KeywordsONCOPROTEIN / Methyltransferase / complex / inhibitor
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 / positive regulation of peptidyl-serine phosphorylation / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
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 / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain ...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 / Zinc finger MYND-type signature. / 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
Diperodon / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCederfelt, D. / Talibov, V.O. / Dobritzsch, D. / Danielson, U.H.
Funding support Sweden, Italy, 2items
OrganizationGrant numberCountry
Swedish Research CouncilD0571301 Sweden
Italian Association for Cancer Research19172 Italy
CitationJournal: Chembiochem / Year: 2021
Title: Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase.
Authors: Talibov, V.O. / Fabini, E. / FitzGerald, E.A. / Tedesco, D. / Cederfeldt, D. / Talu, M.J. / Rachman, M.M. / Mihalic, F. / Manoni, E. / Naldi, M. / Sanese, P. / Forte, G. / Lepore Signorile, ...Authors: Talibov, V.O. / Fabini, E. / FitzGerald, E.A. / Tedesco, D. / Cederfeldt, D. / Talu, M.J. / Rachman, M.M. / Mihalic, F. / Manoni, E. / Naldi, M. / Sanese, P. / Forte, G. / Lepore Signorile, M. / Barril, X. / Simone, C. / Bartolini, M. / Dobritzsch, D. / Del Rio, A. / Danielson, U.H.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SMYD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0999
Polymers48,8311
Non-polymers1,2688
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, monomeric state has been reported in literature by others
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-1 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.142, 66.284, 105.949
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: 48830.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2
References: UniProt: Q9H7B4, [histone H3]-lysine4 N-trimethyltransferase

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Non-polymers , 5 types, 260 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-POW / Diperodon / [(2~{R})-2-(phenylcarbamoyloxy)-3-piperidin-1-yl-propyl] ~{N}-phenylcarbamate


Mass: 397.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: Tris buffer 0.1 M, pH 8.25 Magnesium acetate 0.1 M PEG3350 16%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 1.93→105.95 Å / Num. obs: 32606 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 21.45 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.192 / Rrim(I) all: 0.203 / Net I/av σ(I): 8.9 / Net I/σ(I): 9.99
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.788 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2145 / CC1/2: 0.515 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
REFMAC5refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MEK

3mek


Resolution: 1.93→52.3 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.22
RfactorNum. reflection% reflection
Rfree0.2295 3054 4.97 %
Rwork0.1861 --
obs0.1883 32606 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.99 Å2 / Biso mean: 28.0359 Å2 / Biso min: 11.3 Å2
Refinement stepCycle: final / Resolution: 1.93→52.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 77 256 3735
Biso mean--34.73 31.59 -
Num. residues----425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-1.960.34331310.2926552786100
1.96-1.990.36641260.291826722798100
1.99-2.030.28721630.289226122775100
2.03-2.060.35141570.263326532810100
2.06-2.10.27351770.243925872764100
2.1-2.150.28531250.223727052830100
2.15-2.190.2411480.214326352783100
2.19-2.240.23141470.211126372784100
2.24-2.30.27421500.211126902840100
2.3-2.360.26231380.197426512789100
2.36-2.430.22971210.195426572778100
2.43-2.510.2351660.179326012767100
2.51-2.60.27071060.184427012807100
2.6-2.70.23161140.183226832797100
2.7-2.830.2611080.180526782786100
2.83-2.980.25551280.176526722800100
2.98-3.160.2121470.164626592806100
3.16-3.410.19361520.166126082760100
3.41-3.750.22011280.16472666279499
3.75-4.290.1811550.143626372792100
4.29-5.40.19641330.162826442777100
5.41-52.30.19341340.18422650278499

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