7CJT

Crystal Structure of SETDB1 Tudor domain in complexed with (R,R)-59

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth D]	PF18300	e7cjtD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18300	ECOD (1.6)
A [auth D]	PF18358	e7cjtD2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18358	ECOD (1.6)
A [auth D]	PF18359	e7cjtD3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18359	ECOD (1.6)
B [auth A]	PF18300	e7cjtA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18300	ECOD (1.6)
B [auth A]	PF18358	e7cjtA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18358	ECOD (1.6)
B [auth A]	PF18359	e7cjtA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18359	ECOD (1.6)
C [auth B]	PF18300	e7cjtB3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18300	ECOD (1.6)
C [auth B]	PF18358	e7cjtB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18358	ECOD (1.6)
C [auth B]	PF18359	e7cjtB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18359	ECOD (1.6)
D [auth C]	PF18300	e7cjtC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18300	ECOD (1.6)
D [auth C]	PF18358	e7cjtC3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18358	ECOD (1.6)
D [auth C]	PF18359	e7cjtC2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF18359	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth A], C [auth B], D [auth C]	PF18300	Domain of unknown function (DUF5604) (DUF5604)	Domain of unknown function (DUF5604)	This domain is often found in the N-terminal region of proteins carrying the SET domain (Pfam:PF00856), such as the SETDB1 protein present in Homo sapiens. SETDB1 is a histone methyltransferase that suppresses gene expression and modulates heterochro ...	This domain is often found in the N-terminal region of proteins carrying the SET domain (Pfam:PF00856), such as the SETDB1 protein present in Homo sapiens. SETDB1 is a histone methyltransferase that suppresses gene expression and modulates heterochromatin formation through H3K9me2/3 [1].	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	PF18359	Histone methyltransferase Tudor domain 1 (Tudor_5)	Histone methyltransferase Tudor domain 1	This is the first TUDOR domain found in SETDB1 enzymes (EC:2.1.1.43) in homosapiens, also known as Eggless in Drosophila [1]. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4 [2]. SET domain, bifurcated 1 (SETD ...	This is the first TUDOR domain found in SETDB1 enzymes (EC:2.1.1.43) in homosapiens, also known as Eggless in Drosophila [1]. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4 [2]. SET domain, bifurcated 1 (SETDB1) is a histone methyltransferase (HMT) that methylates lysine 9 on histone H3 (H3K9). The enzymatic activity of SETDB1, in association with MBD1-containing chromatin-associated factor 1 (MCAF1), converts H3K9me2 to H3K9me3 and represses subsequent transcription. SETDB1 is amplified in cancers such as melanoma and lung cancer, and increased expression of SETDB1 promotes tumorigenesis in a zebrafish melanoma model. In addition, SETDB1 is required for endogenous retrovirus silencing during early embryogenesis, inhibition of adipocyte differentiation, and differentiation of mesenchymal cells into osteoblasts [1]. The tandem Tudor domains in the N-terminal region are involved in protein-protein interactions [2]. The second tudor domain is Pfam:PF18385.	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	PF18358	Histone methyltransferase Tudor domain (Tudor_4)	Histone methyltransferase Tudor domain	This is a Tudor domain found in histone-lysine N-methyltransferase SETDB1 proteins (EC:2.1.1.43), also known as Eggless in Drosophila [1]. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4 [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], B [auth A], C [auth B], D [auth C]	Histone-lysine N-methyltransferase SETDB1	protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups histone H3K9 methyltransferase activity transferase activity histone H3K9 trimethyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone 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 histone H3K9 methyltransferase activity transferase activity histone H3K9 trimethyltransferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity histone H3K9 monomethyltransferase activity protein-containing complex binding chromatin binding binding histone H3K9me2 methyltransferase activity promoter-specific chromatin binding DNA binding organic cyclic compound binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	methylation metabolic process protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular process heterochromatin organization cellular component organization or biogenesis positive regulation of organelle organization regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process cellular component biogenesis methylation metabolic process protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular process heterochromatin organization cellular component organization or biogenesis positive regulation of organelle organization regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process cellular component biogenesis organic substance biosynthetic process regulation of heterochromatin formation regulation of biological process regulation of chromatin organization regulation of DNA methylation-dependent heterochromatin formation cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of chromosome organization regulation of organelle organization negative regulation of cellular biosynthetic process positive regulation of chromosome organization regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process regulation of cellular component organization positive regulation of cellular component organization cellular biosynthetic process positive regulation of biological process positive regulation of DNA methylation-dependent heterochromatin formation positive regulation of heterochromatin formation organic substance metabolic process negative regulation of cellular process DNA methylation-dependent heterochromatin formation positive regulation of chromatin organization chromatin remodeling positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation positive regulation of cellular component biogenesis epigenetic regulation of gene expression biological regulation chromosome organization regulation of macromolecule metabolic process gene expression regulation of cellular component biogenesis macromolecule biosynthetic process regulation of cellular biosynthetic process organelle organization negative regulation of biosynthetic process facultative heterochromatin formation viral life cycle negative regulation of RNA biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process primary metabolic process single stranded viral RNA replication via double stranded DNA intermediate organic cyclic compound metabolic process viral genome replication organic cyclic compound biosynthetic process negative regulation of RNA metabolic process regulation of single stranded viral RNA replication via double stranded DNA intermediate RNA metabolic process negative regulation of single stranded viral RNA replication via double stranded DNA intermediate RNA biosynthetic process nucleic acid biosynthetic process negative regulation of viral process viral RNA genome replication viral process regulation of RNA biosynthetic process negative regulation of viral genome replication nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of viral process regulation of viral life cycle regulation of viral genome replication	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cellular anatomical entity cytoplasm nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle cellular anatomical entity cytoplasm nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen intracellular non-membrane-bounded organelle chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth A], C [auth B], D [auth C]	IPR040880	Domain of unknown function DUF5604	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR007728	Pre-SET domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR046341	SET domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C]	IPR002999	Tudor domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR001214	SET domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR047232	Histone-lysine N-methyltransferase SETDB1/2-like, methyl-CpG binding domains	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR003616	Post-SET domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR016177	DNA-binding domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C]	IPR025796	Histone-lysine N-methyltransferase SETDB1	Family
A [auth D], B [auth A], C [auth B], D [auth C]	IPR041291	Histone methyltransferase, Tudor domain 1	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR001739	Methyl-CpG DNA binding	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR041292	Histone methyltransferase, Tudor domain 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D], B [auth A], C [auth B], D [auth C]	Pharos: Q15047	melanoma malignant mesothelioma prostate cancer cutaneous melanoma schizophrenia Anhedonia atypical teratoid rhabdoid tumor lung cancer medulloblastoma neuroblastoma osteosarcoma primary hyperoxaluria type 1 squamous cell carcinoma astrocytic tumor malignant ependymoma melanoma malignant mesothelioma prostate cancer cutaneous melanoma schizophrenia Anhedonia atypical teratoid rhabdoid tumor lung cancer medulloblastoma neuroblastoma osteosarcoma primary hyperoxaluria type 1 squamous cell carcinoma astrocytic tumor malignant ependymoma oligodendroglioma ovarian cancer primitive neuroectodermal tumor psoriasis attention deficit hyperactivity disorder, inattentive type large cell medulloblastoma metabolic syndrome X osteoporosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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 R01GM133198.