6K1K

Human nucleosome core particle with H2A.X S139E variant

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d6k1kb_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d6k1kf_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6k1kc_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d6k1kg_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6k1kd_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d6k1kh_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8070545	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	Histone	e6k1kA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
E	Histone	e6k1kE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
B	Histone_1	e6k1kB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
F	Histone_1	e6k1kF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
C	Histone_1	e6k1kC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
G	Histone_1	e6k1kG1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
D	Histone	e6k1kD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
H	Histone	e6k1kH1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
E	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
B	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
F	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
C	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
G	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
D	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)
H	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, F	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, 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
A, E	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 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 cellular biosynthetic process cellular metabolic 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, F	Histone H4	DNA binding binding organic cyclic compound 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 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 multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process regulation of megakaryocyte differentiation negative regulation of biological process megakaryocyte differentiation cell development regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation anatomical structure development negative regulation of cellular process 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 hemopoiesis negative regulation of developmental process regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	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 CENP-A containing chromatin 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 CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, G	Histone H2AX	protein binding binding histone binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein heterodimerization activity protein dimerization activity DNA binding organic cyclic compound binding damaged DNA binding nucleic acid binding structural molecule activity structural constituent of chromatin protein binding binding histone binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein heterodimerization activity protein dimerization activity DNA binding organic cyclic compound binding damaged DNA binding nucleic acid binding structural molecule activity structural constituent of chromatin protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding enzyme binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus response to gamma radiation protein localization localization cellular localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to site of double-strand break regulation of cellular process positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process DNA repair regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process cellular metabolic process cellular senescence 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 component organization or biogenesis nucleosome assembly nucleosome organization multicellular organismal process head development forebrain development animal organ development brain development nervous system development pallium development cerebral cortex development multicellular organism development central nervous system development anatomical structure development telencephalon development system development double-strand break repair DNA recombination recombinational repair double-strand break repair via homologous recombination cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process regulation of cellular metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process meiotic cell cycle cell cycle DNA damage checkpoint signaling regulation of cell cycle phase transition signaling negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cell communication negative regulation of cell cycle phase transition signal transduction regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen condensed nuclear chromosome nuclear chromosome chromosome intracellular non-membrane-bounded organelle condensed chromosome non-membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton XY body sex chromosome protein-containing complex protein-DNA complex nucleosome chromatin replication fork male germ cell nucleus germ cell nucleus site of double-strand break site of DNA damage
D, H	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 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 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 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 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 response to peptide regulation of response to cytokine 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	DNA (145-MER)	-	-	-
J	DNA (145-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E	IPR009072	Histone-fold	Homologous Superfamily
A, E	IPR007125	Histone H2A/H2B/H3	Domain
A, E	IPR000164	Histone H3/CENP-A	Family
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
C, G	IPR002119	Histone H2A	Family
C, G	IPR032454	Histone H2A, C-terminal domain	Domain
C, G	IPR032458	Histone H2A conserved site	Conserved Site
C, G	IPR009072	Histone-fold	Homologous Superfamily
C, G	IPR007125	Histone H2A/H2B/H3	Domain
D, H	IPR009072	Histone-fold	Homologous Superfamily
D, H	IPR007125	Histone H2A/H2B/H3	Domain
D, H	IPR000558	Histone H2B	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, E	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
B, F	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma 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 acute myeloid leukemia squamous cell lung carcinoma 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 allergic rhinitis ulcerative colitis 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
C, G	Pharos: P16104	glioblastoma breast carcinoma Neoplasm Recurrence, Local polyploidy breast cancer giant cell glioblastoma ovarian cancer atopic eczema cancer ductal breast carcinoma in situ lung adenocarcinoma malignant mesothelioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma psoriasis glioblastoma breast carcinoma Neoplasm Recurrence, Local polyploidy breast cancer giant cell glioblastoma ovarian cancer atopic eczema cancer ductal breast carcinoma in situ lung adenocarcinoma malignant mesothelioma non-small cell lung carcinoma pancreatic ductal adenocarcinoma psoriasis endometriosis heart disease lung cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm schizophrenia invasive ductal breast carcinoma malignant ependymoma
D, H	Pharos: P06899	autism spectrum disorder lung adenocarcinoma breast cancer schizophrenia endogenous depression

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.