Annotations: 9E49

Cryo-EM structure of a di-nucleosome with an eight base-pair linker

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Core histone-like	8070531	3001387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8070531	3001387	SCOP2B (2022-06-29)
I [auth M]	SCOP2B Superfamily	Core histone-like	8070531	3001387	SCOP2B (2022-06-29)
M [auth Q]	SCOP2B Superfamily	Core histone-like	8070531	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)
J [auth N]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
N [auth R]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8067130	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8067130	3001387	SCOP2B (2022-06-29)
K [auth O]	SCOP2B Superfamily	Core histone-like	8067130	3001387	SCOP2B (2022-06-29)
O [auth S]	SCOP2B Superfamily	Core histone-like	8067130	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	WD40	e9e49A1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
E	WD40	e9e49E1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
I [auth M]	WD40	e9e49M1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
M [auth Q]	WD40	e9e49Q1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
B	WD40	e9e49B1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
F	WD40	e9e49F1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
J [auth N]	WD40	e9e49N1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
N [auth R]	WD40	e9e49R1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
C	WD40	e9e49C1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
G	WD40	e9e49G1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
K [auth O]	WD40	e9e49O1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
O [auth S]	WD40	e9e49S1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
D	WD40	e9e49D1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
H	WD40	e9e49H1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
L [auth P]	WD40	e9e49P1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
P [auth T]	WD40	e9e49T1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E, I [auth M], M [auth Q]	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
B, F, J [auth N], N [auth R]	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, K [auth O], O [auth S]	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, I [auth M], M [auth Q]	Histone H3.2	DNA binding protein-containing complex binding binding chromatin binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA 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 regulation of cellular 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 regulation of cellular process negative regulation of biological process negative regulation of cellular process 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 negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle 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
B, F, J [auth N], N [auth R]	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 vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle chromosome, telomeric region chromosomal region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, G, K [auth O], O [auth S]	Histone H2A	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 vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle 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
D, H, L [auth P], P [auth T]	Histone H2B	DNA binding 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 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 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	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus membrane-enclosed lumen protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
Q [auth I]	DNA (314-MER)	-	-	-
R [auth J]	DNA (314-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E, I [auth M], M [auth Q]	IPR009072	Histone-fold	Homologous Superfamily
A, E, I [auth M], M [auth Q]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, E, I [auth M], M [auth Q]	IPR000164	Histone H3/CENP-A	Family
B, F, J [auth N], N [auth R]	IPR009072	Histone-fold	Homologous Superfamily
B, F, J [auth N], N [auth R]	IPR035425	CENP-T/Histone H4, histone fold	Domain
B, F, J [auth N], N [auth R]	IPR001951	Histone H4	Family
B, F, J [auth N], N [auth R]	IPR019809	Histone H4, conserved site	Conserved Site
B, F, J [auth N], N [auth R]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
C, G, K [auth O], O [auth S]	IPR009072	Histone-fold	Homologous Superfamily
C, G, K [auth O], O [auth S]	IPR002119	Histone H2A	Family
C, G, K [auth O], O [auth S]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C, G, K [auth O], O [auth S]	IPR032454	Histone H2A, C-terminal domain	Domain
C, G, K [auth O], O [auth S]	IPR032458	Histone H2A conserved site	Conserved Site
D, H, L [auth P], P [auth T]	IPR009072	Histone-fold	Homologous Superfamily
D, H, L [auth P], P [auth T]	IPR000558	Histone H2B	Family
D, H, L [auth P], P [auth T]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
D, H, L [auth P], P [auth T]	IPR055333	Histone H2B, conserved site	Conserved Site

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.