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- PDB-7bj1: Crystal structure of SMYD3 with diperodon S enantiomer bound to a... -

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Basic information

Entry
Database: PDB / ID: 7bj1
TitleCrystal structure of SMYD3 with diperodon S 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 / metal ion binding / nucleus / 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 superfamily / 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 superfamily / SET domain / SET domain profile. / SET domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ACETATE ION / Diperodon (S-enantiomer) / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsTalibov, V.O. / Cederfelt, D. / 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. / Barril, X. / ...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. / Barril, X. / Simone, C. / Bartolini, M. / Dobritzsch, D. / Danielson, U.H.
History
DepositionJan 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Mar 17, 2021Group: Advisory / Category: pdbx_database_PDB_obs_spr / Item: _pdbx_database_PDB_obs_spr.id
SupersessionMar 21, 2021ID: 6Z2R
Revision 1.3Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _audit_author.name / _citation.country ..._audit_author.name / _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.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)50,75510
Polymers49,4601
Non-polymers1,2949
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-1 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.909, 66.050, 107.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 49460.402 Da / Num. of mol.: 1 / Mutation: K13N, K140R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9H7B4, [histone H3]-lysine4 N-trimethyltransferase

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Non-polymers , 6 types, 532 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-QKT / Diperodon (S-enantiomer)


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


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: Protein: 50 mM Tris, 150 mM NaCl, 1 mM (S)-diperodon, 10% DMSO, pH 8.0; reservoir: 100 mM Tris, 50 mM magnesium acetate, 11% PEG3350, pH 8.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.61→56.24 Å / Num. obs: 56743 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Rrim(I) all: 0.075 / Net I/σ(I): 12.3
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.528 / Num. unique obs: 5473 / CC1/2: 0.466 / Rpim(I) all: 0.765 / Rrim(I) all: 1.714 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PHENIX1.18.2_3874refinement
XDSb. 20180126data reduction
Aimless0.7.1data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CCL

5ccl


Resolution: 1.61→44.78 Å / SU ML: 0.2463 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.21 2730 4.82 %
Rwork0.1715 53911 -
obs0.1734 56641 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 1.61→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 79 523 4010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833591
X-RAY DIFFRACTIONf_angle_d1.13974841
X-RAY DIFFRACTIONf_chiral_restr0.0665530
X-RAY DIFFRACTIONf_plane_restr0.0058623
X-RAY DIFFRACTIONf_dihedral_angle_d22.4818514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.640.45991510.39192750X-RAY DIFFRACTION98.98
1.64-1.670.33911390.33722788X-RAY DIFFRACTION99.76
1.67-1.70.33911310.28812824X-RAY DIFFRACTION99.83
1.7-1.740.25561370.24992793X-RAY DIFFRACTION99.83
1.74-1.780.29811460.23642792X-RAY DIFFRACTION99.8
1.78-1.830.25061570.22662806X-RAY DIFFRACTION99.87
1.83-1.880.23721300.22422818X-RAY DIFFRACTION99.86
1.88-1.930.23981490.21132798X-RAY DIFFRACTION99.97
1.93-1.990.24761660.19182820X-RAY DIFFRACTION99.9
1.99-2.070.21441120.18262841X-RAY DIFFRACTION99.86
2.07-2.150.22651450.17392809X-RAY DIFFRACTION99.76
2.15-2.250.2281420.16552848X-RAY DIFFRACTION99.83
2.25-2.360.21361460.16822833X-RAY DIFFRACTION99.93
2.36-2.510.21271390.17112837X-RAY DIFFRACTION99.9
2.51-2.710.20321520.17452843X-RAY DIFFRACTION99.97
2.71-2.980.22731350.16192880X-RAY DIFFRACTION99.97
2.98-3.410.20021560.15832879X-RAY DIFFRACTION99.87
3.41-4.290.16631610.13462891X-RAY DIFFRACTION99.64
4.3-44.780.17451360.14933061X-RAY DIFFRACTION99.63

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