8QKT

Structure of a nucleosome composed of a palindromic 167-base pair blunt-ended DNA fragment

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 [auth AAA]	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
E [auth EEE]	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
K [auth KKK]	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
O [auth OOO]	SCOP2B Superfamily	Core histone-like	8039340	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 [auth AAA]	PF00125	e8qktAAA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
E [auth EEE]	PF00125	e8qktEEE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
K [auth KKK]	PF00125	e8qktKKK1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
O [auth OOO]	PF00125	e8qktOOO1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
B [auth BBB]	PF15511	e8qktBBB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
F [auth FFF]	PF15511	e8qktFFF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
L [auth LLL]	PF15511	e8qktLLL1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
P [auth PPP]	PF15511	e8qktPPP1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
C [auth CCC]	PF00125,PF16211	e8qktCCC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
M [auth MMM]	PF00125,PF16211	e8qktMMM1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
D [auth DDD]	PF00125	e8qktDDD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
N [auth NNN]	PF00125	e8qktNNN1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
G [auth GGG]	PF00125,PF16211	e8qktGGG1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
Q [auth QQQ]	PF00125,PF16211	e8qktQQQ1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
H [auth HHH]	PF00125	e8qktHHH1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
R [auth RRR]	PF00125	e8qktRRR1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AAA], E [auth EEE], K [auth KKK], O [auth OOO]	Histone H3.1	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 organic substance metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	membrane cellular anatomical entity 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 membrane cellular anatomical entity 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 chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B [auth BBB], F [auth FFF], L [auth LLL], P [auth PPP]	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 CCC], M [auth MMM]	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	negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process	protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin cellular anatomical entity chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome organelle intracellular non-membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin cellular anatomical entity chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome organelle intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
D [auth DDD], N [auth NNN]	Histone H2B type 1-J	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity lipid binding lipopolysaccharide binding carbohydrate derivative binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 protein-DNA complex organization cellular component 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 disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response to Gram-negative bacterium defense response to bacterium response to bacterium antibacterial humoral response protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin cellular response to stimulus response to organic substance regulation of cellular process negative regulation of signaling signaling negative regulation of biological process response to cytokine regulation of signal transduction negative regulation of cell communication cytokine-mediated signaling pathway cell communication cellular response to tumor necrosis factor negative regulation of cellular process tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction cellular response to organic substance regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway negative regulation of response to stimulus regulation of cytokine-mediated signaling pathway biological regulation negative regulation of tumor necrosis factor-mediated signaling pathway negative regulation of signal transduction regulation of response to cytokine stimulus cellular response to chemical stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus negative regulation of cytokine-mediated signaling pathway response to chemical regulation of cell communication response to tumor necrosis factor defense response to Gram-positive bacterium	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome organelle intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
G [auth GGG], Q [auth QQQ]	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
H [auth HHH], R [auth RRR]	Histone H2B type 1-J	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity lipid binding lipopolysaccharide binding carbohydrate derivative binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 protein-DNA complex organization cellular component 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 disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response to Gram-negative bacterium defense response to bacterium response to bacterium antibacterial humoral response protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin cellular response to stimulus response to organic substance regulation of cellular process negative regulation of signaling signaling negative regulation of biological process response to cytokine regulation of signal transduction negative regulation of cell communication cytokine-mediated signaling pathway cell communication cellular response to tumor necrosis factor negative regulation of cellular process tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction cellular response to organic substance regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway negative regulation of response to stimulus regulation of cytokine-mediated signaling pathway biological regulation negative regulation of tumor necrosis factor-mediated signaling pathway negative regulation of signal transduction regulation of response to cytokine stimulus cellular response to chemical stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus negative regulation of cytokine-mediated signaling pathway response to chemical regulation of cell communication response to tumor necrosis factor defense response to Gram-positive bacterium	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome organelle intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
I [auth III], S [auth SSS]	DNA (167-MER)	-	-	-
J [auth JJJ], T [auth TTT]	DNA (167-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AAA], E [auth EEE], K [auth KKK], O [auth OOO]	IPR009072	Histone-fold	Homologous Superfamily
A [auth AAA], E [auth EEE], K [auth KKK], O [auth OOO]	IPR007125	Histone H2A/H2B/H3	Domain
A [auth AAA], E [auth EEE], K [auth KKK], O [auth OOO]	IPR000164	Histone H3/CENP-A	Family
B [auth BBB], F [auth FFF], L [auth LLL], P [auth PPP]	IPR009072	Histone-fold	Homologous Superfamily
B [auth BBB], F [auth FFF], L [auth LLL], P [auth PPP]	IPR001951	Histone H4	Family
B [auth BBB], F [auth FFF], L [auth LLL], P [auth PPP]	IPR035425	CENP-T/Histone H4, histone fold	Domain
B [auth BBB], F [auth FFF], L [auth LLL], P [auth PPP]	IPR019809	Histone H4, conserved site	Conserved Site
B [auth BBB], F [auth FFF], L [auth LLL], P [auth PPP]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
C [auth CCC], M [auth MMM]	IPR009072	Histone-fold	Homologous Superfamily
C [auth CCC], M [auth MMM]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth CCC], M [auth MMM]	IPR002119	Histone H2A	Family
C [auth CCC], M [auth MMM]	IPR032454	Histone H2A, C-terminal domain	Domain
C [auth CCC], M [auth MMM]	IPR032458	Histone H2A conserved site	Conserved Site
D [auth DDD], N [auth NNN]	IPR009072	Histone-fold	Homologous Superfamily
D [auth DDD], N [auth NNN]	IPR007125	Histone H2A/H2B/H3	Domain
D [auth DDD], N [auth NNN]	IPR000558	Histone H2B	Family
G [auth GGG], Q [auth QQQ]	IPR009072	Histone-fold	Homologous Superfamily
G [auth GGG], Q [auth QQQ]	IPR007125	Histone H2A/H2B/H3	Domain
G [auth GGG], Q [auth QQQ]	IPR002119	Histone H2A	Family
G [auth GGG], Q [auth QQQ]	IPR032454	Histone H2A, C-terminal domain	Domain
G [auth GGG], Q [auth QQQ]	IPR032458	Histone H2A conserved site	Conserved Site
H [auth HHH], R [auth RRR]	IPR009072	Histone-fold	Homologous Superfamily
H [auth HHH], R [auth RRR]	IPR007125	Histone H2A/H2B/H3	Domain
H [auth HHH], R [auth RRR]	IPR000558	Histone H2B	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth AAA], E [auth EEE], K [auth KKK], O [auth OOO]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pancreatic intraductal papillary-mucinous carcinoma astrocytoma (excluding glioblastoma) spina bifida breast cancer cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor subependymoma breast carcinoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
D [auth DDD], N [auth NNN]	Pharos: P06899	autism spectrum disorder lung adenocarcinoma breast cancer schizophrenia endogenous depression
H [auth HHH], R [auth RRR]	Pharos: P06899	autism spectrum disorder lung adenocarcinoma breast cancer schizophrenia endogenous depression