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- PDB-8q5p: Structure of the lysine methyltransferase SETD2 in complex with a... -

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Basic information

Entry
Database: PDB / ID: 8q5p
TitleStructure of the lysine methyltransferase SETD2 in complex with a peptide derived from human tyrosine kinase ACK1
Components
  • Activated CDC42 kinase 1
  • Histone-lysine N-methyltransferase SETD2
KeywordsTRANSFERASE / Histone methyltransferase
Function / homology
Function and homology information


mesoderm morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / coronary vasculature morphogenesis / regulation of clathrin-dependent endocytosis / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / Grb2-EGFR complex / embryonic placenta morphogenesis ...mesoderm morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / coronary vasculature morphogenesis / regulation of clathrin-dependent endocytosis / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / Grb2-EGFR complex / embryonic placenta morphogenesis / histone H3K36 trimethyltransferase activity / cytoophidium / GTPase inhibitor activity / pericardium development / regulation of mRNA export from nucleus / stem cell development / histone H3K36 methyltransferase activity / nucleosome organization / response to type I interferon / protein-lysine N-methyltransferase activity / embryonic cranial skeleton morphogenesis / positive regulation of ossification / response to alkaloid / regulation of protein localization to chromatin / response to metal ion / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / histone H3 methyltransferase activity / positive regulation of peptidyl-tyrosine phosphorylation / WW domain binding / phosphorylation / regulation of double-strand break repair via homologous recombination / small GTPase-mediated signal transduction / endodermal cell differentiation / positive regulation of interferon-alpha production / alpha-tubulin binding / mismatch repair / forebrain development / clathrin-coated pit / positive regulation of autophagy / protein serine/threonine/tyrosine kinase activity / cytoplasmic vesicle membrane / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / adherens junction / non-membrane spanning protein tyrosine kinase activity / stem cell differentiation / neural tube closure / non-specific protein-tyrosine kinase / transcription elongation by RNA polymerase II / : / PKMTs methylate histone lysines / endocytosis / chromosome / regulation of gene expression / protein tyrosine kinase activity / angiogenesis / defense response to virus / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / protein serine kinase activity / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / regulation of DNA-templated transcription / perinuclear region of cytoplasm / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / : / SAM domain-like ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / : / SAM domain-like / Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / TFIIS/LEDGF domain superfamily / Post-SET domain / Post-SET domain profile. / Variant SH3 domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Activated CDC42 kinase 1 / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.814 Å
AuthorsMechaly, A. / Le Coadou, L. / Dupret, J.M. / Haouz, A. / Rodrigues Lima, F.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural and enzymatic evidence for the methylation of the ACK1 tyrosine kinase by the histone lysine methyltransferase SETD2.
Authors: Le Coadou, L. / Berthelet, J. / Mechaly, A.E. / Michail, C. / Bui, L.C. / Dairou, J. / Haouz, A. / Dupret, J.M. / Rodrigues Lima, F.
History
DepositionAug 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD2
B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0416
Polymers35,4462
Non-polymers5954
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-24 kcal/mol
Surface area13910 Å2
Unit cell
Length a, b, c (Å)60.94, 76.33, 77.41
Angle α, β, γ (deg.)90, 90, 90
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 (E. coli)
References: UniProt: Q9BYW2, histone-lysine N-methyltransferase
#2: Protein/peptide Activated CDC42 kinase 1 / ACK-1 / Tyrosine kinase non-receptor protein 2


Mass: 1347.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q07912, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M TRIS pH 8.5, 16%w/v PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.814→34.52 Å / Num. obs: 33159 / % possible obs: 99.36 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06118 / Rpim(I) all: 0.01759 / Rrim(I) all: 0.06371 / Net I/σ(I): 21.58
Reflection shellResolution: 1.814→1.879 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 3091 / CC1/2: 0.835 / Rpim(I) all: 0.3376 / Rrim(I) all: 1.229 / % possible all: 94.23

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.814→40.56 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1658 -RANDOM
Rwork0.2163 ---
obs0.2178 33160 99.3 %-
Displacement parametersBiso mean: 48.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.8406 Å20 Å20 Å2
2---7.1864 Å20 Å2
3---8.027 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.814→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 30 174 2256
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082121HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.952848HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d770SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2121HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion260SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1805SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion17.76
LS refinement shellResolution: 1.814→1.83 Å
RfactorNum. reflection% reflection
Rfree0.2183 33 -
Rwork0.2444 --
obs--75.71 %
Refinement TLS params.Origin x: -13.3846 Å / Origin y: -5.1205 Å / Origin z: 3.0299 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °
Refinement TLS groupSelection details: { A|* }

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