Entry Database : PDB / ID : 5ex3 Structure visualization Downloads & linksTitle Crystal structure of human SMYD3 in complex with a VEGFR1 peptide ComponentsHistone-lysine N-methyltransferase SMYD3 VEGFR1 peptide DetailsKeywords TRANSFERASE / SET domain / methylation / chromatin / cancerFunction / homology Function and homology informationFunction Domain/homology Component
vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity ... vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / histone H3K4 trimethyltransferase activity / negative regulation of vascular endothelial cell proliferation / blood vessel morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / growth factor binding / monocyte chemotaxis / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / : / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / cellular response to dexamethasone stimulus / positive regulation of MAP kinase activity / establishment of protein localization / receptor protein-tyrosine kinase / PKMTs methylate histone lysines / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / nucleosome assembly / cell migration / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / methylation / angiogenesis / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / receptor complex / endosome / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / focal adhesion / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function Vascular endothelial growth factor receptor 1 (VEGFR1) / Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain ... Vascular endothelial growth factor receptor 1 (VEGFR1) / Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Annexin V; domain 1 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / Helix Hairpins / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Beta Complex / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Helix non-globular / Immunoglobulin V-Type / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Immunoglobulin V-set domain / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology ACETIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / Vascular endothelial growth factor receptor 1 / Histone-lysine N-methyltransferase SMYD3 Similarity search - ComponentBiological species Homo sapiens (human)Method X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution : 2.408 Å DetailsAuthors Qiao, Q. / Fu, W. / Liu, N. / Wang, M. / Min, J. / Zhu, B. / Xu, R.M. / Yang, N. Funding support China, 6items Details Hide detailsOrganization Grant number Country MOST 2015CB856200 China National Natural Science Foundation of China 31521002 China National Natural Science Foundation of China 31430018 China National Natural Science Foundation of China 31210103914 China Strategic priority research program of CAS XDB08010100 China National key new drug creation and manufacturing program of China 2014ZX09507002 China
CitationJournal : J.Biol.Chem. / Year : 2016Title : Structural Basis for Substrate Preference of SMYD3, a SET Domain-containing Protein Lysine MethyltransferaseAuthors : Fu, W. / Liu, N. / Qiao, Q. / Wang, M. / Min, J. / Zhu, B. / Xu, R.M. / Yang, N. History Deposition Nov 23, 2015 Deposition site : RCSB / Processing site : PDBJRevision 1.0 Mar 9, 2016 Provider : repository / Type : Initial releaseRevision 1.1 May 25, 2016 Group : Database referencesRevision 1.2 Oct 18, 2017 Group : Author supporting evidence / Database references / Derived calculationsCategory : citation / pdbx_audit_support / pdbx_struct_oper_listItem : _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
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