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- PDB-5lsx: Structure of the Epigenetic Oncogene MMSET and inhibition by N-Al... -

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Basic information

Entry
Database: PDB / ID: 5lsx
TitleStructure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives
ComponentsHistone-lysine N-methyltransferase SETD2
KeywordsTRANSFERASE / lysine methyltransferase SETD2 SET domain / SETD2#1
Function / homology
Function and homology information


mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus ...mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus / pericardium development / stem cell development / nucleosome organization / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / response to type I interferon / positive regulation of ossification / embryonic cranial skeleton morphogenesis / response to alkaloid / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / alpha-tubulin binding / positive regulation of interferon-alpha production / mismatch repair / positive regulation of autophagy / forebrain development / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / neural tube closure / transcription elongation by RNA polymerase II / stem cell differentiation / response to organic cyclic compound / PKMTs methylate histone lysines / chromosome / regulation of gene expression / angiogenesis / defense response to virus / regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain / Set2 Rpb1 interacting domain superfamily / SRI (Set2 Rpb1 interacting) domain / SETD2/Set2, SET domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Beta-clip-like ...Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain / Set2 Rpb1 interacting domain superfamily / SRI (Set2 Rpb1 interacting) domain / SETD2/Set2, SET domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Beta-clip-like / SET domain / TFIIS/LEDGF domain superfamily / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET domain superfamily / WW domain / SET domain / SET domain profile. / SET domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-76O / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsTisi, D. / Pathuri, P. / Heightman, T.
CitationJournal: ACS Chem. Biol. / Year: 2016
Title: Structure of the Epigenetic Oncogene MMSET and Inhibition by N-Alkyl Sinefungin Derivatives.
Authors: Tisi, D. / Chiarparin, E. / Tamanini, E. / Pathuri, P. / Coyle, J.E. / Hold, A. / Holding, F.P. / Amin, N. / Martin, A.C. / Rich, S.J. / Berdini, V. / Yon, J. / Acklam, P. / Burke, R. / ...Authors: Tisi, D. / Chiarparin, E. / Tamanini, E. / Pathuri, P. / Coyle, J.E. / Hold, A. / Holding, F.P. / Amin, N. / Martin, A.C. / Rich, S.J. / Berdini, V. / Yon, J. / Acklam, P. / Burke, R. / Drouin, L. / Harmer, J.E. / Jeganathan, F. / van Montfort, R.L. / Newbatt, Y. / Tortorici, M. / Westlake, M. / Wood, A. / Hoelder, S. / Heightman, T.D.
History
DepositionSep 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7695
Polymers34,0991
Non-polymers6704
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.244, 77.305, 78.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-lysine N-methyltransferase SETD2 / HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin- ...HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin-interacting protein B / Lysine N-methyltransferase 3A / SET domain-containing protein 2 / hSET2 / p231HBP


Mass: 34098.812 Da / Num. of mol.: 1 / Fragment: UNP residues 1433-1711
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus RIL
References: UniProt: Q9BYW2, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-76O / [(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium


Mass: 473.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H31N7O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Hepes, pH 7.3, 0.1MKSCN, 25-30%MPEG2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→55.19 Å / Num. obs: 54976 / % possible obs: 99.7 % / Redundancy: 6.3 % / Net I/σ(I): 15.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.9→36.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.913 / SU B: 42.795 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R Free: 0.44 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28025 340 4.8 %RANDOM
Rwork0.17947 ---
obs0.1844 6695 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 122.365 Å2
Baniso -1Baniso -2Baniso -3
1-11 Å20 Å2-0 Å2
2---9.12 Å20 Å2
3----1.88 Å2
Refinement stepCycle: 1 / Resolution: 2.9→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 37 7 1887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191924
X-RAY DIFFRACTIONr_bond_other_d0.0030.021758
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9422586
X-RAY DIFFRACTIONr_angle_other_deg0.9582.9754055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.295230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93824.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.34215.299351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1231515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2265
X-RAY DIFFRACTIONr_gen_planes_refined00.0212196
X-RAY DIFFRACTIONr_gen_planes_other00.021470
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.64119.824923
X-RAY DIFFRACTIONr_mcbond_other7.64519.827922
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.07221.3261001
X-RAY DIFFRACTIONr_scbond_other9.06721.3261002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined15.76144.577698
X-RAY DIFFRACTIONr_long_range_B_other15.84844.581685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.556 21 -
Rwork0.397 466 -
obs--99.59 %
Refinement TLS params.Method: refined / Origin x: -1.6682 Å / Origin y: 15.3907 Å / Origin z: -14.9249 Å
111213212223313233
T0.1698 Å20.0938 Å20.0391 Å2-0.0942 Å20.0088 Å2--0.0164 Å2
L3.33 °22.1184 °2-0.9789 °2-9.2738 °2-1.2922 °2--3.3441 °2
S-0.2617 Å °-0.1277 Å °-0.0809 Å °-0.2072 Å °0.1587 Å °-0.0336 Å °0.1429 Å °0.0657 Å °0.103 Å °

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