9NQU | pdb_00009nqu

KDM6B-nucleosome structure stabilized by H3K27C-UNC8015 covalent conjugate

External Resource: Annotation

Domain Annotation: SCOP2 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)
H	SCOP2B Superfamily	Core histone-like	8066267	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8066267	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8067130	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8067130	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8070531	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8070531	3001387	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
K	PF21322	Lysine-specific demethylase 6/UTY, C-terminal helical domain (KDM6_C-hel)	Lysine-specific demethylase 6/UTY, C-terminal helical domain	Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry incudes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also ...	Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry incudes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also known as JMJD3) and the related histone demethylase UTY [[1-4]. This is the C-terminal helical domain localised adjacent the JmjC domain.	Domain
K	PF02373	JmjC domain, hydroxylase (JmjC)	JmjC domain, hydroxylase	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the ...	The JmjC domain belongs to the Cupin superfamily [3]. JmjC-domain proteins may be protein hydroxylases that catalyse a novel histone modification [4]. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation [5].	Domain
K	PF21326	KDM6, GATA-like (KDM6_GATAL)	KDM6, GATA-like	Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry includes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also ...	Histone lysine (K) demethylases (KDMs) catalyse the demethylation of lysine residue from histone tails. This entry includes KDM6 subfamily that contains a conserved catalytic Jumonji C (JmjC) domain and includes KDM6A (also known as UTX), KDM6B (also known as JMJD3) and the related histone demethylase UTY (also known as KMD6C) [1,2]. This entry represents the Zn2+-coordinated GATA-like (GATAL) domain [1,2], which seems to be sensitive to redox environment. It is involved in substrate binding [3].	Domain
C, G	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
K	Lysine-specific demethylase 6B	chromatin binding binding sequence-specific DNA binding DNA binding nucleic acid binding catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity chromatin binding binding sequence-specific DNA binding DNA binding nucleic acid binding catalytic activity, acting on a protein protein demethylase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen histone demethylase activity demethylase activity dioxygenase activity oxidoreductase activity histone H3 demethylase activity histone modifying activity histone H3K27me2/H3K27me3 demethylase activity catalytic activity 2-oxoglutarate-dependent dioxygenase activity beta-catenin binding protein binding cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development multicellular organism development central nervous system development anatomical structure development telencephalon development hippocampus development limbic system development developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development multicellular organism development central nervous system development anatomical structure development telencephalon development hippocampus development limbic system development system development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process response to stimulus response to activity heart development cellular developmental process cardiac muscle tissue development cardiac muscle cell differentiation muscle cell differentiation tissue development cardiocyte differentiation striated muscle tissue development circulatory system development muscle structure development cell differentiation striated muscle cell differentiation muscle tissue development epithelium development endothelial cell differentiation endothelium development epithelial cell differentiation cellular response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress response to stress response to chemical homeostatic process positive regulation of biological process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of cellular process defense response immune response immune system process inflammatory response inflammatory response to antigenic stimulus response to antibiotic response to fungicide response to toxic substance cell fate commitment formation of primary germ layer mesodermal cell differentiation mesoderm morphogenesis embryonic morphogenesis embryo development gastrulation tissue morphogenesis anatomical structure morphogenesis anatomical structure formation involved in morphogenesis mesoderm formation mesoderm development 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 DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II 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 transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen
J	DNA (185-MER)	-	-	-
I	DNA (185-MER)	-	-	-
D, H	Histone H2B type 1-C/E/F/G/I	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin identical protein binding	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 biological process involved in interspecies interaction between organisms 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 biological process involved in interspecies interaction between organisms innate immune response in mucosa response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus mucosal immune response organ or tissue specific immune response humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide antibacterial humoral response defense response to bacterium response to bacterium defense response to Gram-positive bacterium	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol protein-containing complex extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol protein-containing complex protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, G	Histone H2A type 1	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity enzyme binding 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	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus intracellular membrane-bounded organelle
B, F	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity RNA binding 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 organelle organization 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 organelle organization telomere organization chromosome organization localization protein localization to chromatin protein localization to chromosome protein localization to chromosome, centromeric region protein localization to organelle macromolecule localization protein localization to CENP-A containing chromatin intracellular protein localization multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process regulation of megakaryocyte differentiation negative regulation of biological process cell development megakaryocyte differentiation regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome membraneless organelle chromosome, centromeric region chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, E	Histone H3.2	DNA binding binding nucleic acid binding chromatin 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 biosynthetic process 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 biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule 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 transcription by RNA polymerase II 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process	cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless 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
K	IPR048562	Lysine-specific demethylase 6A/B-like, C-terminal helical domain	Domain
K	IPR003347	JmjC domain	Domain
K	IPR046941	Lysine-specific demethylase 6, GATA-like domain superfamily	Homologous Superfamily
K	IPR048560	Lysine-specific demethylase 6A/B-like, GATA-like	Domain
K	IPR051630	Transcriptional Corepressor and Histone Demethylase	Family
D, H	IPR009072	Histone-fold	Homologous Superfamily
D, H	IPR000558	Histone H2B	Family
D, H	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
D, H	IPR055333	Histone H2B, conserved site	Conserved Site
C, G	IPR009072	Histone-fold	Homologous Superfamily
C, G	IPR002119	Histone H2A	Family
C, G	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C, G	IPR032454	Histone H2A, C-terminal domain	Domain
C, G	IPR032458	Histone H2A conserved site	Conserved Site
B, F	IPR009072	Histone-fold	Homologous Superfamily
B, F	IPR035425	CENP-T/Histone H4, histone fold	Domain
B, F	IPR001951	Histone H4	Family
B, F	IPR019809	Histone H4, conserved site	Conserved Site
B, F	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
A, E	IPR009072	Histone-fold	Homologous Superfamily
A, E	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, E	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D, H	Pharos: P62807	breast carcinoma lung adenocarcinoma breast cancer lung carcinoma Malignant neoplasm of breast ovarian cancer ulcerative colitis autism spectrum disorder exocrine pancreatic carcinoma hypertensive disorder malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma psoriasis allergic rhinitis breast carcinoma lung adenocarcinoma breast cancer lung carcinoma Malignant neoplasm of breast ovarian cancer ulcerative colitis autism spectrum disorder exocrine pancreatic carcinoma hypertensive disorder malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma psoriasis allergic rhinitis cutaneous lupus erythematosus ductal breast carcinoma in situ glioblastoma interstitial cystitis lung cancer malignant mesothelioma osteoarthritis squamous cell lung carcinoma atypical teratoid rhabdoid tumor cystic fibrosis endogenous depression gout invasive ductal breast carcinoma
C, G	Pharos: P0C0S8	malignant pancreatic neoplasm ovarian cancer psoriasis acne benign prostatic hyperplasia chronic obstructive pulmonary disease exocrine pancreatic carcinoma glioblastoma lung cancer malignant glioma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast cancer malignant pancreatic neoplasm ovarian cancer psoriasis acne benign prostatic hyperplasia chronic obstructive pulmonary disease exocrine pancreatic carcinoma glioblastoma lung cancer malignant glioma medulloblastoma pancreatic intraductal papillary-mucinous carcinoma squamous cell lung carcinoma atypical teratoid rhabdoid tumor breast cancer cutaneous lupus erythematosus gastric cancer hepatocellular carcinoma lung carcinoma malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm autism spectrum disorder breast carcinoma endogenous depression gastric carcinoma lung adenocarcinoma malignant colon neoplasm
B, F	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pilocytic astrocytoma ulcerative colitis allergic rhinitis autism spectrum disorder cystic fibrosis endogenous depression glioblastoma hypertensive disorder lung cancer malignant mesothelioma multiple sclerosis osteosarcoma psoriasis astrocytic tumor breast cancer diabetes mellitus endometriosis gout invasive ductal breast carcinoma
A, E	Pharos: Q71DI3	idiopathic scoliosis