5HQ2

Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
D [auth H]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00125	e5hq2A1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
B	PF15511	e5hq2B1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
C [auth G]	PF00125,PF16211	e5hq2G1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
D [auth H]	PF00125	e5hq2H1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
G [auth K]	PF00415	e5hq2K1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00415	ECOD (1.6)
H [auth M]	PF00856	e5hq2M1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: PF00856	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
B	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain
C [auth G]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
C [auth G]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
D [auth H]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
G [auth K]	PF00415	Regulator of chromosome condensation (RCC1) repeat (RCC1)	Regulator of chromosome condensation (RCC1) repeat	-	Repeat
G [auth K]	PF13540	Regulator of chromosome condensation (RCC1) repeat (RCC1_2)	Regulator of chromosome condensation (RCC1) repeat	-	Repeat
H [auth M]	PF00856	SET domain (SET)	SET domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Histone H3.2	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B	Histone H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C [auth G]	Histone H2A	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
D [auth H]	Histone H2B 1.1	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
E [auth I]	DNA (149-MER)	-	-	-
F [auth J]	DNA (149-MER)	-	-	-
G [auth K]	Guanine nucleotide exchange factor SRM1	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	cellular process cell cycle cellular localization nitrogen compound transport nucleocytoplasmic transport transport cellular biosynthetic process nuclear transport mRNA transport localization organic substance metabolic process mRNA export from nucleus establishment of localization in cell organic substance biosynthetic process cellular process cell cycle cellular localization nitrogen compound transport nucleocytoplasmic transport transport cellular biosynthetic process nuclear transport mRNA transport localization organic substance metabolic process mRNA export from nucleus establishment of localization in cell organic substance biosynthetic process RNA localization nuclear export nucleobase-containing compound transport RNA transport organic substance transport cellular metabolic process nucleic acid transport poly(A)+ mRNA export from nucleus intracellular transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process macromolecule localization metabolic process macromolecule metabolic process response to organic substance response to stimulus response to chemical response to pheromone cell division establishment of organelle localization ribonucleoprotein complex biogenesis ribosomal subunit export from nucleus protein-containing complex localization cellular component biogenesis ribosome biogenesis organelle localization cellular component organization or biogenesis ribosome localization cellular component organization nucleus organization organelle organization protein localization establishment of protein localization protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport cellular macromolecule localization protein localization to organelle protein import into nucleus intracellular protein transport	intracellular anatomical structure cytoplasm cellular anatomical entity intracellular organelle protein-containing complex protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
H [auth M]	N-lysine methyltransferase SETD8	histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity protein-lysine N-methyltransferase activity histone H4K20 methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity lysine N-methyltransferase activity N-methyltransferase activity histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity protein-lysine N-methyltransferase activity histone H4K20 methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity lysine N-methyltransferase activity N-methyltransferase activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity histone H4K20 monomethyltransferase activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process cellular response to stimulus regulation of DNA recombination response to stimulus regulation of double-strand break repair regulation of cellular response to stress negative regulation of DNA repair cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair recombinational repair negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair double-strand break repair negative regulation of response to stimulus DNA recombination DNA metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination DNA damage response regulation of response to stimulus negative regulation of DNA metabolic process regulation of DNA metabolic process cell division mitotic nuclear division mitotic chromosome condensation organelle fission chromosome organization sister chromatid segregation mitotic cell cycle cellular component organization organelle organization nuclear division mitotic cell cycle process chromosome condensation mitotic sister chromatid segregation nuclear chromosome segregation cell cycle cellular component organization or biogenesis chromosome segregation cell cycle process signaling regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator regulation of signaling signal transduction by p53 class mediator regulation of cell communication signal transduction in response to DNA damage peptidyl-lysine methylation organonitrogen compound metabolic process protein methylation peptidyl-lysine modification peptidyl-lysine monomethylation macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle polytene chromosome chromosome cellular anatomical entity non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle polytene chromosome chromosome cellular anatomical entity non-membrane-bounded organelle cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex protein-DNA complex chromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR009072	Histone-fold	Homologous Superfamily
A	IPR007125	Histone H2A/H2B/H3	Domain
A	IPR000164	Histone H3/CENP-A	Family
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR001951	Histone H4	Family
B	IPR035425	CENP-T/Histone H4, histone fold	Domain
B	IPR019809	Histone H4, conserved site	Conserved Site
B	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
C [auth G]	IPR009072	Histone-fold	Homologous Superfamily
C [auth G]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth G]	IPR002119	Histone H2A	Family
C [auth G]	IPR032454	Histone H2A, C-terminal domain	Domain
C [auth G]	IPR032458	Histone H2A conserved site	Conserved Site
D [auth H]	IPR009072	Histone-fold	Homologous Superfamily
D [auth H]	IPR007125	Histone H2A/H2B/H3	Domain
D [auth H]	IPR000558	Histone H2B	Family
G [auth K]	IPR000408	Regulator of chromosome condensation, RCC1	Repeat
G [auth K]	IPR009091	Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II	Homologous Superfamily
H [auth M]	IPR046341	SET domain superfamily	Homologous Superfamily
H [auth M]	IPR001214	SET domain	Domain
H [auth M]	IPR016858	N-lysine methyltransferase KMT5A-like	Family
H [auth M]	IPR047266	N-lysine methyltransferase KMT5A-like, SET domain	Domain