6ICT | pdb_00006ict

Structure of SETD3 bound to SAH and methylated actin

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	SET_5	e6ictD1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET_5	ECOD (1.6)
D	Rubis-subs-bind	e6ictD2	A: a+b complex topology	X: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	H: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	T: RuBisCo LSMT C-terminal, substrate-binding domain	F: Rubis-subs-bind	ECOD (1.6)
C	SET_5	e6ictC2	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET_5	ECOD (1.6)
C	Rubis-subs-bind	e6ictC1	A: a+b complex topology	X: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	H: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	T: RuBisCo LSMT C-terminal, substrate-binding domain	F: Rubis-subs-bind	ECOD (1.6)
B	SET_5	e6ictB1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET_5	ECOD (1.6)
B	Rubis-subs-bind	e6ictB2	A: a+b complex topology	X: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	H: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	T: RuBisCo LSMT C-terminal, substrate-binding domain	F: Rubis-subs-bind	ECOD (1.6)
A	SET_5	e6ictA1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET_5	ECOD (1.6)
A	Rubis-subs-bind	e6ictA2	A: a+b complex topology	X: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	H: RuBisCo LSMT C-terminal, substrate-binding domain (From Topology)	T: RuBisCo LSMT C-terminal, substrate-binding domain	F: Rubis-subs-bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (utative)
D	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (utative)
C	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (utative)
C	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (utative)
B	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (utative)
B	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (utative)
A	3.90.1410.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 1	set domain protein methyltransferase, domain 1	CATH (utative)
A	3.90.1420.10	Alpha Beta	Alpha-Beta Complex	set domain protein methyltransferase, domain 2	Rubisco LSMT, substrate-binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00856	SET domain (SET)	SET domain	-	Family
A, B, C, D	PF09273	Rubisco LSMT substrate-binding (Rubis-subs-bind)	Rubisco LSMT substrate-binding	Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco ho ...	Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Histone-lysine N-methyltransferase setd3	protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K4 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K4 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity cytoskeletal protein binding actin binding protein binding binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity histone H3K36 methyltransferase activity protein-L-histidine N-tele-methyltransferase activity	multicellular organismal process system process regulation of biological process regulation of system process biological regulation muscle contraction muscle system process regulation of muscle system process uterine smooth muscle contraction smooth muscle contraction regulation of smooth muscle contraction regulation of muscle contraction regulation of uterine smooth muscle contraction regulation of multicellular organismal process multicellular organismal process system process regulation of biological process regulation of system process biological regulation muscle contraction muscle system process regulation of muscle system process uterine smooth muscle contraction smooth muscle contraction regulation of smooth muscle contraction regulation of muscle contraction regulation of uterine smooth muscle contraction regulation of multicellular organismal process actin cytoskeleton organization primary metabolic process cellular component organization organelle organization actin modification macromolecule modification actin filament-based process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular component organization or biogenesis protein modification process cytoskeleton organization developmental process regulation of cellular process regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation muscle cell differentiation positive regulation of muscle cell differentiation muscle structure development positive regulation of developmental process regulation of muscle cell differentiation positive regulation of cell differentiation cell differentiation anatomical structure development positive regulation of cellular process protein methylation macromolecule methylation protein alkylation methylation peptidyl-histidine modification peptidyl-amino acid modification peptidyl-histidine methylation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome
E, F [auth G], G [auth H], H [auth I]	Actin, cytoplasmic 1	structural constituent of postsynapse structural constituent of cytoskeleton structural molecule activity structural constituent of synapse structural constituent of postsynaptic actin cytoskeleton binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding structural constituent of postsynapse structural constituent of cytoskeleton structural molecule activity structural constituent of synapse structural constituent of postsynaptic actin cytoskeleton binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cytoskeletal protein binding protein binding tau protein binding enzyme regulator activity molecular function regulator activity nitric-oxide synthase regulator activity nitric-oxide synthase binding enzyme binding identical protein binding kinesin binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding Tat protein binding kinase binding protein kinase binding transporter regulator activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	regulation of chromosome segregation regulation of cell cycle phase transition regulation of cellular process regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation regulation of chromosome segregation regulation of cell cycle phase transition regulation of cellular process regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation cell cycle process regulation of biological process regulation of cell cycle process biological regulation chromosome organization sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition organelle organization mitotic cell cycle process regulation of sister chromatid segregation nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle cellular process metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition developmental process regulation of developmental process cellular developmental process positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development regulation of myoblast differentiation myoblast differentiation positive regulation of cellular process multicellular organismal process regulation of body fluid levels wound healing response to stimulus homotypic cell-cell adhesion cell activation hemostasis platelet aggregation blood coagulation cell adhesion cell-cell adhesion response to stress coagulation regulation of biological quality response to wounding platelet activation regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death cellular response to nitrogen compound cellular response to stimulus response to cytochalasin B response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to cytochalasin B cellular response to chemical stimulus response to chemical regulation of localization import into cell cellular localization transport synaptic vesicle cycle regulation of synaptic vesicle recycling vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse localization synaptic vesicle recycling regulation of synaptic vesicle endocytosis establishment of localization in cell regulation of endocytosis synaptic vesicle endocytosis regulation of transport regulation of vesicle-mediated transport establishment of localization endocytosis axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis system development plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development tissue morphogenesis epithelium development morphogenesis of a polarized epithelium morphogenesis of an epithelium tissue development cytoskeleton organization regulation of DNA recombination regulation of double-strand break repair regulation of cellular response to stress positive regulation of double-strand break repair via homologous recombination regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair cellular response to stress regulation of response to stress recombinational repair positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process double-strand break repair via homologous recombination DNA repair positive regulation of DNA recombination double-strand break repair DNA recombination primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair regulation of double-strand break repair via homologous recombination positive regulation of DNA metabolic process DNA damage response regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process monoamine transport norepinephrine transport nitrogen compound transport organic hydroxy compound transport organic cation transport catecholamine uptake catecholamine transport regulation of norepinephrine uptake norepinephrine uptake establishment or maintenance of cell polarity protein localization to cell periphery regulation of protein localization protein localization to plasma membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization macromolecule localization intracellular protein localization regulation of protein localization to plasma membrane regulation of protein localization to membrane negative regulation of developmental process negative regulation of biological process negative regulation of cellular process negative regulation of cell differentiation cell motility adherens junction organization adherens junction assembly cellular component biogenesis cell junction organization cellular component assembly cell junction assembly cell-cell junction assembly cell-cell junction organization transepithelial transport regulation of transepithelial transport apical protein localization positive regulation of norepinephrine uptake positive regulation of transport regulation of stem cell population maintenance stem cell population maintenance positive regulation of stem cell population maintenance positive regulation of multicellular organismal process regulation of multicellular organismal process maintenance of cell number cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation head development animal organ development brain development substantia nigra development central nervous system development midbrain development neural nucleus development nucleotide-excision repair regulation of nucleotide-excision repair positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of G0 to G1 transition G0 to G1 transition maintenance of blood-brain barrier multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis protein localization to cell junction protein localization to adherens junction protein localization to cell-cell junction transcription by RNA polymerase II regulation of transcription by RNA polymerase II regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development positive regulation of cell activation T cell activation positive regulation of leukocyte activation T cell differentiation regulation of immune system process positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion leukocyte differentiation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation positive regulation of hemopoiesis regulation of cell-cell adhesion regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation immune system process regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation chromatin organization chromatin remodeling	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle organelle membraneless organelle SWI/SNF superfamily-type complex brahma complex GBAF complex extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoskeleton actin cytoskeleton cytoplasm cytosol SWI/SNF complex apical part of cell cluster of actin-based cell projections brush border synapse glutamatergic synapse apical junction complex adherens junction nBAF complex axon neuron projection axon terminus presynapse distal axon calyx of Held neuron projection terminus npBAF complex polymeric cytoskeletal fiber actin filament supramolecular fiber supramolecular polymer supramolecular complex cell cortex cortical cytoskeleton cell periphery membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear lumen nuclear matrix focal adhesion cell-substrate junction postsynapse postsynaptic cytoskeleton postsynaptic actin cytoskeleton NuA4 histone acetyltransferase complex transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex protein acetyltransferase complex intracellular protein-containing complex RSC-type complex dense body plasma membrane protein-DNA complex nucleosome nucleoplasm bBAF complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule blood microparticle chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region condensed chromosome Schaffer collateral - CA1 synapse tight junction ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR046341	SET domain superfamily	Homologous Superfamily
A, B, C, D	IPR015353	Rubisco LSMT, substrate-binding domain	Domain
A, B, C, D	IPR001214	SET domain	Domain
A, B, C, D	IPR044428	SETD3, SET domain	Domain
A, B, C, D	IPR025785	Actin-histidine N-methyltransferase SETD3	Family
A, B, C, D	IPR050600	SETD3/SETD6 methyltransferase	Family
A, B, C, D	IPR036464	Rubisco LSMT, substrate-binding domain superfamily	Homologous Superfamily
E, F [auth G], G [auth H], H [auth I]	IPR020902	Actin/actin-like conserved site	Conserved Site
E, F [auth G], G [auth H], H [auth I]	IPR004001	Actin, conserved site	Conserved Site
E, F [auth G], G [auth H], H [auth I]	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
E, F [auth G], G [auth H], H [auth I]	IPR004000	Actin family	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q86TU7	colorectal cancer
E, F [auth G], G [auth H], H [auth I]	Pharos: P60709	developmental malformations-deafness-dystonia syndrome coloboma dystonic disorder Baraitser-Winter cerebrofrontofacial syndrome intellectual disability Neoplasm Invasiveness Baraitser-Winter syndrome 1 carcinoma dysostosis esophageal cancer sarcomatoid carcinoma ovarian cancer central nervous system malformation large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm developmental malformations-deafness-dystonia syndrome coloboma dystonic disorder Baraitser-Winter cerebrofrontofacial syndrome intellectual disability Neoplasm Invasiveness Baraitser-Winter syndrome 1 carcinoma dysostosis esophageal cancer sarcomatoid carcinoma ovarian cancer central nervous system malformation large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm liver disease plasma cell myeloma lung disease prostate disease schizophrenia drug-induced liver injury mammary neoplasms, animal arthritic joint disease stomach disease multiple endocrine neoplasia type 2A atypical teratoid rhabdoid tumor uterine disease glioblastoma obesity disorder Borst-Jadassohn intraepidermal carcinoma hepatocellular carcinoma ovarian disease cerebrovascular disorder linear and whorled nevoid hypermelanosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia colonic disease lung adenocarcinoma primary cutaneous amyloidosis coronary artery disease rheumatoid arthritis craniosynostosis malignant ependymoma seborrheic keratosis malignant pancreatic neoplasm skin basal cell carcinoma astrocytic tumor type 2 diabetes mellitus mycosis fungoides autoimmune disease vertebral column disease neoplasm of esophagus Becker nevus syndrome head and neck cancer hyperglycemia osteoarthritis breast disease osteosarcoma kidney disease pancreatic ductal adenocarcinoma chronic obstructive pulmonary disease pilocytic astrocytoma lung benign neoplasm primitive neuroectodermal tumor lymphatic system disease dermatomyositis malignant glioma Down syndrome skin disease medulloblastoma atherosclerosis undifferentiated carcinoma myocardial ischemia X-linked mixed deafness with perilymphatic gusher eye disease neurodegenerative disease bipolar disorder hematologic disease hypertensive disorder osteoarthritis susceptibility 1 cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F [auth G], G [auth H], H [auth I]	HIC	Parent Component: HIS RESID: AA0317 PSI-MOD : 1'-methyl-L-histidine MOD:00322

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.