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- PDB-7qnu: SMYD3 in complex with fragment FL08619 -

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Basic information

Entry
Database: PDB / ID: 7qnu
TitleSMYD3 in complex with fragment FL08619
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 profile. / SET domain superfamily / SET domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
BENZOYL-FORMIC ACID / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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)50,2056
Polymers49,4601
Non-polymers7455
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-4 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.931, 65.886, 105.085
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-173 / BENZOYL-FORMIC ACID / OXO(PHENYL)ACETIC ACID


Mass: 150.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.1 Å3/Da / Density % sol: 41.35 % / Description: needle
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: ID23-1 / Wavelength: 0.976256 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976256 Å / Relative weight: 1
ReflectionResolution: 1.64→41.08 Å / Num. obs: 48981 / % possible obs: 74.97 % / Redundancy: 6.2 % / Biso Wilson estimate: 16.27 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.2142 / Net I/σ(I): 6.45
Reflection shellResolution: 1.64→1.699 Å / Num. unique obs: 149 / CC1/2: 0.134 / Rpim(I) all: 1.548

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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: 1.64→41.08 Å / SU ML: 0.1734 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 1987 5.13 %
Rwork0.1846 36757 -
obs0.1869 38744 74.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.61 Å2
Refinement stepCycle: LAST / Resolution: 1.64→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 41 445 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853550
X-RAY DIFFRACTIONf_angle_d0.87444791
X-RAY DIFFRACTIONf_chiral_restr0.0504526
X-RAY DIFFRACTIONf_plane_restr0.0116625
X-RAY DIFFRACTIONf_dihedral_angle_d21.7871499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.347440.312147X-RAY DIFFRACTION1.39
1.68-1.720.2831190.2856281X-RAY DIFFRACTION8.23
1.72-1.770.3383520.2686941X-RAY DIFFRACTION27.04
1.77-1.830.30631130.26152045X-RAY DIFFRACTION58.55
1.83-1.890.29571290.24012524X-RAY DIFFRACTION72.03
1.89-1.970.28451610.23132921X-RAY DIFFRACTION83.96
1.97-2.060.23931740.2073168X-RAY DIFFRACTION89.86
2.06-2.170.29571690.1853353X-RAY DIFFRACTION96.07
2.17-2.30.23161860.17993528X-RAY DIFFRACTION99.7
2.3-2.480.21181990.17393523X-RAY DIFFRACTION99.81
2.48-2.730.23811920.18113543X-RAY DIFFRACTION99.84
2.73-3.130.22652020.17193550X-RAY DIFFRACTION99.73
3.13-3.940.19961880.15883580X-RAY DIFFRACTION99.5
3.94-41.080.20131990.18423753X-RAY DIFFRACTION99.45
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)
10.582426424046-0.390039579895-0.6485255313451.82342154654-0.02619880307832.68998498339-0.0225432640478-0.0764758303387-0.0699275723580.05700246647440.08604906327680.2882159609150.0840300308565-0.132355611163-0.05599474074560.08704603053960.0120278316133-0.03764095545390.1203045626530.02032144513690.1416964162143.415430449025.5740514064221.4704209027
22.415061273050.6414068401790.1250599634183.101112508761.153594090012.198067710130.1134578346150.231464182383-0.243727777286-0.2628998454440.000354138552563-0.3079120437390.237036383880.283729466605-0.08668093100240.2484562306850.0597980006364-0.01859045420080.12002496332-0.04492249009310.15224714844215.6289660908-2.04342024245-6.0259781534
32.560223555831.165891238061.195095591257.949866654691.60955502561.42635656642-0.09728450360.1384987859720.291516646375-0.5996764489750.1937769952330.5322182153850.094294422244-0.00670274309896-0.1067177120740.236607240342-0.0135373796465-0.04908245078810.132302816495-0.01678160531370.1601501705598.269127620466.27452209835-8.36520168261
41.888038851490.3786625721620.02807532648021.566753790770.3346807029281.96115961658-0.07594113118290.0867164625858-0.00886896657622-0.1851728507790.091655941-0.0226395156496-0.05291008896620.0679521944131-0.01021662140890.09999120305880.00344585919635-0.02330592783290.06079954067630.004719597352760.082942147195214.166129679616.90781349715.21271484359
50.865537124848-0.01646817154870.09930785900941.4736476041-0.2186498251071.123607925510.03898314655790.0265872263995-0.022548045838-0.1264757960320.001499532831480.04849982685570.0812705565562-0.0194811851203-0.03539837238780.08739783818250.0137576571604-0.03491455737660.092920973837-0.008925907820110.078475456536311.63888446558.8957100146210.4656705949
60.739982552538-0.440719759077-0.237439052631.15157877651-0.1047379993220.454899350591-0.0278060890786-0.06764320382180.0630630805296-0.004218483545050.0372490304999-0.08925342705210.04389923220850.0448554933479-0.0128919340380.1092125333160.00552574107198-0.04051867388070.109895793905-0.003254414528580.096126960448628.1305728452-4.3293493830119.9008691978
70.389750956376-0.0250580870494-0.1865192000253.602618222120.4678324472580.8858948279220.0329206854894-0.012440081163-0.355641604526-0.1828265759950.01685590089310.2598480260990.111255723067-0.0226461273169-0.01731913568870.1574181580220.00141953752813-0.06985549918920.08972413356640.006423562299910.20048172267212.9686217526-21.128814744716.7884859596
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 - 92}73 - 9271 - 90
44{A|93 - 155}93 - 15591 - 153
55{A|156 - 225}156 - 225154 - 223
66{A|226 - 366}226 - 366224 - 364
77{A|367 - 428}367 - 428365 - 426

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