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- PDB-7qlb: SMYD3 in complex with fragment FL06268 -

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Basic information

Entry
Database: PDB / ID: 7qlb
TitleSMYD3 in complex with fragment FL06268
ComponentsHistone-lysine N-methyltransferase SMYD3
KeywordsTRANSFERASE / methyltransferase / epigenetic / oncogen / histone
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
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. / 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 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
1-methylimidazole-4-sulfonamide / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLund, B.A. / Cederfelt, D. / Dobritzsch, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675899European Union
CitationJournal: Rsc Med Chem / Year: 2024
Title: Identification of fragments targeting SMYD3 using highly sensitive kinetic and multiplexed biosensor-based screening
Authors: FitzGerald, E.A. / Cederfelt, D. / Lund, B.A. / Myers, N. / Zhang, H. / Dobritzsch, D. / Danielson, H.
History
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 24, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,3777
Polymers49,4601
Non-polymers9176
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.938, 66.329, 108.165
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

#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
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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-E4I / 1-methylimidazole-4-sulfonamide


Mass: 161.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.34 % / Description: needles
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.25-8.75 0.1M Magnesium acetate 15-18 % PEG 3350
PH range: 8.25-8.75 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.8→29.33 Å / Num. obs: 82041 / % possible obs: 99.21 % / Redundancy: 2 % / Biso Wilson estimate: 21.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.01908 / Rrim(I) all: 0.02698 / Net I/σ(I): 24.1
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1444 / Mean I/σ(I) obs: 4.87 / Num. unique obs: 7484 / CC1/2: 0.95 / Rrim(I) all: 0.2042 / % possible all: 93.17

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
BUSTER2.10.4refinement
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6z2r

6z2r
PDB Unreleased entry


Resolution: 1.8→29.33 Å / SU ML: 0.1645 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5062
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1833 1945 4.74 %
Rwork0.1503 39082 -
obs0.1519 41027 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 50 510 3968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913564
X-RAY DIFFRACTIONf_angle_d0.9634816
X-RAY DIFFRACTIONf_chiral_restr0.0574531
X-RAY DIFFRACTIONf_plane_restr0.0077631
X-RAY DIFFRACTIONf_dihedral_angle_d20.4712492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.25011200.19482521X-RAY DIFFRACTION91.48
1.85-1.890.22771230.17962749X-RAY DIFFRACTION98.49
1.89-1.950.2331260.16032787X-RAY DIFFRACTION99.97
1.95-2.010.20481430.15292753X-RAY DIFFRACTION99.9
2.01-2.090.22161460.14912774X-RAY DIFFRACTION100
2.09-2.170.17721320.14692791X-RAY DIFFRACTION99.9
2.17-2.270.1761550.14392770X-RAY DIFFRACTION99.86
2.27-2.390.18781440.14142796X-RAY DIFFRACTION99.93
2.39-2.540.19871290.14372799X-RAY DIFFRACTION99.97
2.54-2.730.17641430.15022798X-RAY DIFFRACTION99.93
2.73-3.010.20531530.15422832X-RAY DIFFRACTION99.97
3.01-3.440.16611660.14872809X-RAY DIFFRACTION100
3.44-4.330.15211210.13492895X-RAY DIFFRACTION100
4.33-29.330.17971440.16043008X-RAY DIFFRACTION99.78
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)
10.851305365148-0.0222995992104-0.678200958520.8809712961340.07318463898644.69063005619-0.04417686375280.0490141312267-0.0571209608201-0.1144130700620.04937280140540.0690675923420.310923836586-0.002521838759980.02461969655830.1445474206380.00351400338622-0.04673012801120.1611440319040.009433515042730.20347645984510.09799011082.000557491518.54106355263
21.57273387347-0.6801261699871.658766061284.504846772111.634591477123.17842717354-0.09306498953350.2913574811420.0674093375535-0.448691816510.113732496401-0.126836381787-0.1745099120080.217967491240.02234069877570.208539905846-0.04080803116690.02772333555960.215737009620.009234116492790.1527871232613.08490235599.80448371665-5.60982646744
32.594536302230.66330875778-0.2742417920991.69110021543-0.0141360257513.04839115-0.06331495426390.1477428912420.0750690604383-0.1482032637160.0719618487340.0647554237502-0.182677007791-0.1253389646060.005002663815290.1283981126620.0299995321081-0.0213019204720.09609192899580.002198556657010.15505534198214.042560003620.29134363395.94313441481
40.713747546922-0.5110441325190.3312526610091.07368368223-0.2661724268610.6438614862790.08936673002150.0202759577359-0.121850561418-0.0687227484222-0.02532217265540.06760503096820.170787437380.0211741367414-0.04534942015980.147000204345-0.00161833461003-0.01141428351370.1185685348610.004172289992190.12069462175422.0985870635-6.7527872844518.4430770992
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11{A|3 - 72}3 - 721 - 70
22{A|73 - 114}73 - 11471 - 112
33{A|115 - 170}115 - 170113 - 168
44{A|171 - 428}171 - 428169 - 426

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