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- PDB-7qnr: SMYD3 in complex with fragment FL01791 -

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Basic information

Entry
Database: PDB / ID: 7qnr
TitleSMYD3 in complex with fragment FL01791
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 / 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 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
3-propan-2-yl-1,2,4-thiadiazol-5-amine / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 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)50,1986
Polymers49,4601
Non-polymers7385
Water6,125340
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 area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.236, 66.218, 105.302
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-SAM / S-ADENOSYLMETHIONINE


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-E45 / 3-propan-2-yl-1,2,4-thiadiazol-5-amine


Mass: 143.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.12 Å3/Da / Density % sol: 42.06 % / 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: ESRF / Beamline: ID30B / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.57→44.56 Å / Num. obs: 233855 / % possible obs: 97.8 % / Redundancy: 4 % / Biso Wilson estimate: 22.49 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1338 / Rpim(I) all: 0.07183 / Net I/σ(I): 7.03
Reflection shellResolution: 1.57→1.626 Å / Rmerge(I) obs: 2.605 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5660 / CC1/2: 0.171 / Rpim(I) all: 1.373

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Processing

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

6z2r
PDB Unreleased entry


Resolution: 1.57→44.56 Å / SU ML: 0.2601 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 28.5946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 2090 1.96 %
Rwork0.2035 104669 -
obs0.2041 106759 93.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.62 Å2
Refinement stepCycle: LAST / Resolution: 1.57→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 39 340 3787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613553
X-RAY DIFFRACTIONf_angle_d0.82774798
X-RAY DIFFRACTIONf_chiral_restr0.045529
X-RAY DIFFRACTIONf_plane_restr0.0196624
X-RAY DIFFRACTIONf_dihedral_angle_d20.9962499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.33941270.39526189X-RAY DIFFRACTION81.94
1.6-1.640.3821390.35986950X-RAY DIFFRACTION93.34
1.64-1.690.37341430.35577166X-RAY DIFFRACTION94.91
1.69-1.740.30721490.33747148X-RAY DIFFRACTION95.75
1.74-1.790.38121450.33517199X-RAY DIFFRACTION95.92
1.79-1.860.32241420.30417133X-RAY DIFFRACTION95.3
1.86-1.930.30531410.26047124X-RAY DIFFRACTION95.34
1.93-2.020.32071450.23537274X-RAY DIFFRACTION96.49
2.02-2.120.23741430.2157177X-RAY DIFFRACTION95.91
2.12-2.260.27961440.19157138X-RAY DIFFRACTION94.88
2.26-2.430.20871380.18357030X-RAY DIFFRACTION93.85
2.43-2.680.27711290.17916877X-RAY DIFFRACTION91.74
2.68-3.060.19611390.1746886X-RAY DIFFRACTION91.87
3.06-3.860.17621360.16036687X-RAY DIFFRACTION89.17
3.86-44.560.18461300.16786691X-RAY DIFFRACTION89.04
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)
10.389866104683-0.345669286145-0.277812023441.61419498798-0.1921731348642.039851960640.00054574113023-0.0888641774644-0.08654390624070.01780620484540.09221438662120.27387041290.0493642528877-0.101839920045-0.09767310244310.1422863062340.00148042414935-0.0354098710030.2310455940330.03399415038430.2696660419113.429957924545.5818820053421.4996680477
24.960507954741.375163485261.679419511363.682537800210.2236842213515.245586582380.007129649178020.275503461838-0.228355479113-0.4026770503960.102906836675-0.3004374387470.1551565217660.241933534052-0.1053320819010.3765918222270.07154239264110.02094153688190.249691896073-0.04032548257450.24496796219715.6749540232-2.01411260873-6.08059039986
31.73479456649-0.26208888241.125399695845.217949420991.650185198122.734646954870.1548325124190.206940227255-0.173993255983-0.443645161332-0.04118899522420.03474426842740.04090395873550.0660897486023-0.07087471438810.25995442736-0.00897480960107-0.02118356618710.2015827304460.01130497054980.16507067161211.39967791339.75148181002-5.20219102921
42.273681127490.965566339963-0.2322502605832.04853000686-0.1510762885232.739091938430.00428226168397-0.0330948375798-0.0348261479734-0.07036477743520.0443435356005-0.0426004339061-0.09246302999010.0916352978907-0.05305709027590.1294567437520.037538273167-0.009129855133190.09624154560690.003056109006060.14882319029814.239152422919.14798140929.62622304505
50.5263439403930.04263199342310.02913262726572.17595360908-0.5521800236630.981724164540.03654447386630.055763322806-0.0464324301992-0.2027731136530.03189697816130.1000456447980.0556192804875-0.0545617587905-0.0857397901260.1792702119260.0100745503425-0.04094250959480.207776471967-0.002210970039090.18554875971611.70257514419.0331270495510.2362409928
61.46858788626-1.01805484980.2014693552921.21921234169-0.1178327723910.401343630501-0.0604831693639-0.09754871015350.0821124463470.1254907988090.0573799208446-0.02868075982030.04046856725010.04761115424710.0009881298608630.2121475413830.0230712303505-0.02565578470360.216028106465-0.01148090485150.21434228827421.52572152044.4912590940327.6835879965
72.13964345370.8368091044811.825610984961.786193412270.8307318917462.25096321547-0.3822665533650.2084081529480.508740632592-0.11125206478-0.0881406280841-0.191904570079-0.8005660109910.1977689480540.6187471802480.3015076240910.0149852434868-0.02509312030280.2501006799850.02305936581640.30777483443136.5329519501-1.4194649737613.5952699755
82.52070718861-0.152673507489-0.3504587673311.844662845120.0345533184042.0017540108-0.01687772878170.02548152883250.0242383732901-0.171487319867-0.0120055886432-0.1023932329590.07240772714050.02784150324570.03898180240590.1921218649460.0272807789248-0.01987543301390.1721346420460.001179390854280.20438848110831.0227835469-12.590791824215.5679256561
93.47742627309-2.22740921315-0.4253880350016.078459919551.194553901371.82953236305-0.025027339595-0.0919352577701-0.4216994642270.0239557261560.03551703522120.3939566076920.124244100605-0.0392654420388-0.00658475398860.183757214738-0.0201486501078-0.05251385567610.1700171519550.01779248479810.21784452433914.7837937885-19.062793324817.9339075234
103.6878031159-2.214140526790.1373565508452.36733532859-2.275391327824.39800149606-0.131037798504-0.0720509474256-0.62623261344-0.2588599297730.1066163296210.3467213754220.16947226097-0.165172672416-0.07774015795480.246564450641-0.0329499115344-0.04633649423980.279240809301-0.010227711170.3703044337619.04278688258-26.075245436514.5395369371
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 - 40}3 - 401 - 38
22{A|41 - 72}41 - 7239 - 70
33{A|73 - 114}73 - 11471 - 112
44{A|115 - 154}115 - 154113 - 152
55{A|155 - 225}155 - 225153 - 223
66{A|226 - 279}226 - 279224 - 277
77{A|280 - 299}280 - 299278 - 297
88{A|300 - 360}300 - 366298 - 364
99{A|367 - 408}367 - 408365 - 406
1010{A|409 - 428}409 - 428407 - 426

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