5HQ2 | pdb_00005hq2

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)
D [auth H]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8041272	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)
H [auth M]	SET	e5hq2M1	A: beta barrels	X: beta-clip	H: SET domain-like (From Topology)	T: SET domain-like	F: SET	ECOD (1.6)
G [auth K]	RCC1	e5hq2K1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: RCC1	ECOD (1.6)
D [auth H]	Histone	e5hq2H1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
C [auth G]	Histone_1	e5hq2G1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
B	Histone_1	e5hq2B1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
A	Histone	e5hq2A1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
H [auth M]	PF00856	SET domain (SET)	SET domain	-	Family
G [auth K]	PF25390	RCC1-like domain (WD40_RLD)	RCC1-like domain	-	Repeat
C [auth G]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
A	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular 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 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 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 cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin
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 localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport 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 cellular process metabolic process macromolecule metabolic process regulation of mitotic cell cycle regulation of biological process regulation of cellular process biological regulation cell cycle regulation of cell cycle mitotic cell cycle response to stimulus response to chemical response to pheromone cell division establishment of organelle localization ribonucleoprotein complex biogenesis ribosomal subunit export from nucleus cellular component biogenesis ribosome biogenesis organelle localization cellular component organization or biogenesis ribosome localization regulation of cytoskeleton organization regulation of cellular component organization microtubule cytoskeleton organization regulation of mitotic spindle organization membraneless organelle assembly cellular component organization cellular component assembly regulation of mitotic spindle assembly mitotic sister chromatid segregation chromosome segregation microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process mitotic nuclear division organelle assembly regulation of cell cycle process organelle fission regulation of microtubule-based process chromosome organization sister chromatid segregation regulation of spindle organization regulation of cellular component biogenesis spindle assembly regulation of organelle organization mitotic spindle organization regulation of spindle assembly mitotic spindle assembly organelle organization nuclear division mitotic cell cycle process regulation of organelle assembly nuclear chromosome segregation microtubule-based process cytoskeleton organization regulation of microtubule cytoskeleton organization nucleus organization establishment of protein localization protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
F [auth J]	DNA (149-MER)	-	-	-
E [auth I]	DNA (149-MER)	-	-	-
D [auth H]	Histone H2B 1.1	DNA binding 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 intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C [auth G]	Histone H2A	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A	Histone H3.2	DNA binding 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 intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus membrane-enclosed lumen protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
H [auth M]	IPR051760	Histone-lysine N-methyltransferase KMT5A	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
G [auth K]	IPR058923	RCC1-like domain	Domain
G [auth K]	IPR051553	Ran GTPase-activating	Family
D [auth H]	IPR009072	Histone-fold	Homologous Superfamily
D [auth H]	IPR055333	Histone H2B, conserved site	Conserved Site
D [auth H]	IPR000558	Histone H2B	Family
D [auth H]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C [auth G]	IPR009072	Histone-fold	Homologous Superfamily
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
C [auth G]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
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
A	IPR009072	Histone-fold	Homologous Superfamily
A	IPR000164	Histone H3/CENP-A	Family
A	IPR007125	Core Histone H2A/H2B/H3 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
H [auth M]	Pharos: Q9NQR1	osteoarthritis osteosarcoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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