3X1V

Crystal structure of nucleosome core particle in the presence of histone variant involved in reprogramming

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Core histone-like	8039342	3001387	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Core histone-like	8039342	3001387	SCOP2B (2022-06-29)
F [auth D]	SCOP2 Family	Nucleosome core histones	8066274	4000793	SCOP2 (2022-06-29)
F [auth D]	SCOP2 Superfamily	Core histone-like	8066275	3001387	SCOP2 (2022-06-29)
J [auth H]	SCOP2B Superfamily	Core histone-like	8066275	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)
C [auth A]	Histone	e3x1vA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
G [auth E]	Histone	e3x1vE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
D [auth B]	Histone_1	e3x1vB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
H [auth F]	Histone_1	e3x1vF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
E [auth C]	Histone_1	e3x1vC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
I [auth G]	Histone_1	e3x1vG1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
F [auth D]	Histone	e3x1vD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
J [auth H]	Histone	e3x1vH1	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)
C [auth A]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
G [auth E]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
D [auth B]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
H [auth F]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
E [auth C]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
I [auth G]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
F [auth D]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
J [auth H]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth B], H [auth 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
E [auth C], I [auth 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 [auth I], B [auth J]	DNA (146-MER)	-	-	-
C [auth A], G [auth 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
D [auth B], H [auth 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
E [auth C], I [auth G]	Histone H2A type 1-B/E	DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA 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 cellular biosynthetic process negative regulation of cellular metabolic process cellular component organization chromatin organization chromatin remodeling 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 cellular biosynthetic process negative regulation of cellular metabolic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule 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 metabolic process macromolecule metabolic process regulation of metabolic process 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	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity 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 nucleus intracellular membrane-bounded organelle
F [auth D], J [auth H]	Histone H2B type 1-A	DNA binding binding organic cyclic compound binding nucleic acid binding protein binding histone 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 spermatid development 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 spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation cell differentiation anatomical structure development sperm DNA condensation developmental process multicellular organismal reproductive process male gamete generation nucleus organization organelle organization germ cell development spermatid nucleus differentiation chromosome organization leukocyte migration immune system process mononuclear cell migration cell migration cell motility response to stimulus defense response response to stress inflammatory response cellular component disassembly protein-DNA complex disassembly protein-containing complex disassembly nucleosome disassembly zymogen activation cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process plasminogen activation	cell surface cellular anatomical entity membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus germ cell nucleus intracellular membrane-bounded organelle female germ cell nucleus protein-containing complex protein-DNA complex nucleosome chromatin cell surface cellular anatomical entity membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus germ cell nucleus intracellular membrane-bounded organelle female germ cell nucleus protein-containing complex protein-DNA complex nucleosome chromatin chromosome intracellular non-membrane-bounded organelle non-membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], G [auth E]	IPR009072	Histone-fold	Homologous Superfamily
C [auth A], G [auth E]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth A], G [auth E]	IPR000164	Histone H3/CENP-A	Family
D [auth B], H [auth F]	IPR009072	Histone-fold	Homologous Superfamily
D [auth B], H [auth F]	IPR035425	CENP-T/Histone H4, histone fold	Domain
D [auth B], H [auth F]	IPR001951	Histone H4	Family
D [auth B], H [auth F]	IPR019809	Histone H4, conserved site	Conserved Site
D [auth B], H [auth F]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
E [auth C], I [auth G]	IPR009072	Histone-fold	Homologous Superfamily
E [auth C], I [auth G]	IPR007125	Histone H2A/H2B/H3	Domain
E [auth C], I [auth G]	IPR002119	Histone H2A	Family
E [auth C], I [auth G]	IPR032454	Histone H2A, C-terminal domain	Domain
E [auth C], I [auth G]	IPR032458	Histone H2A conserved site	Conserved Site
F [auth D], J [auth H]	IPR009072	Histone-fold	Homologous Superfamily
F [auth D], J [auth H]	IPR007125	Histone H2A/H2B/H3	Domain
F [auth D], J [auth H]	IPR000558	Histone H2B	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A], G [auth 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
D [auth B], H [auth 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
E [auth C], I [auth G]	Pharos: P04908	juvenile idiopathic arthritis pituitary cancer acute myeloid leukemia autism spectrum disorder hypertensive disorder lung adenocarcinoma medulloblastoma ovarian cancer psoriasis allergic rhinitis breast cancer invasive ductal breast carcinoma Juvenile psoriatic arthritis lung cancer non-small cell lung carcinoma juvenile idiopathic arthritis pituitary cancer acute myeloid leukemia autism spectrum disorder hypertensive disorder lung adenocarcinoma medulloblastoma ovarian cancer psoriasis allergic rhinitis breast cancer invasive ductal breast carcinoma Juvenile psoriatic arthritis lung cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma squamous cell lung carcinoma atypical teratoid rhabdoid tumor ductal breast carcinoma in situ lung carcinoma osteoarthritis

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.