5WCU | pdb_00005wcu

Crystal structure of 167 bp nucleosome bound to the globular domain of linker histone H5

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)
O	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Core histone-like	8067128	3001387	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Core histone-like	8067128	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8067128	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8067128	3001387	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	Winged helix DNA-binding domain	8002931	3000034	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	Winged helix DNA-binding domain	8002931	3000034	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)
O	Histone	e5wcuO1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
K	Histone	e5wcuK1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
E	Histone	e5wcuE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
A	Histone	e5wcuA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
P	Histone_1	e5wcuP1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
L	Histone_1	e5wcuL1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
F	Histone_1	e5wcuF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
B	Histone_1	e5wcuB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
Q	Histone_1	e5wcuQ1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
M	Histone_1	e5wcuM1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
G	Histone_1	e5wcuG1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
C	Histone_1	e5wcuC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
R	Histone	e5wcuR1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
N	Histone	e5wcuN1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
H	Histone	e5wcuH1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
D	Histone	e5wcuD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
V	Linker_histone	e5wcuV1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Linker_histone	ECOD (1.6)
U	Linker_histone	e5wcuU1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Linker_histone	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E, K, O	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
B, F, L, P	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, M, Q	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
C, G, M, Q	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
D, H, N, R	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
U, V	PF00538	linker histone H1 and H5 family (Linker_histone)	linker histone H1 and H5 family	Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E, K, O	Histone H3	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	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle RCAF complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle RCAF complex protein-DNA complex nucleosome chromatin
B, F, L, P	Histone H4	DNA binding binding nucleic acid 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	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex nuclear protein-containing complex RCAF complex protein-DNA complex nucleosome chromatin
C, G, M, Q	Histone H2A	DNA binding binding nucleic acid 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 developmental process muscle structure development multicellular organism development multicellular organismal process somatic muscle development larval somatic muscle development anatomical structure development larval development post-embryonic development	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome chromosomal region polytene chromosome band protein-containing complex protein-DNA complex nucleosome chromatin intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome chromosomal region polytene chromosome band protein-containing complex protein-DNA complex nucleosome chromatin membrane-bounded organelle nucleus intracellular membrane-bounded organelle
D, H, N, R	Histone H2B	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity protein-containing complex binding structural molecule activity structural constituent of chromatin	cellular component organization chromatin organization cellular process cellular component organization or biogenesis	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 intracellular membrane-bounded organelle
I, S	DNA (167-MER)	-	-	-
J, T	DNA (167-MER)	-	-	-
U, V	Histone H5	DNA binding double-stranded DNA binding binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA 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 chromosome condensation chromosome organization regulation of DNA recombination regulation of cellular process negative regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of metabolic process DNA recombination biological regulation primary metabolic process regulation of macromolecule metabolic process DNA metabolic process nucleic acid metabolic process negative regulation of DNA recombination negative regulation of DNA metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process	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 intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E, K, O	IPR009072	Histone-fold	Homologous Superfamily
A, E, K, O	IPR000164	Histone H3/CENP-A	Family
A, E, K, O	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B, F, L, P	IPR009072	Histone-fold	Homologous Superfamily
B, F, L, P	IPR035425	CENP-T/Histone H4, histone fold	Domain
B, F, L, P	IPR001951	Histone H4	Family
B, F, L, P	IPR019809	Histone H4, conserved site	Conserved Site
B, F, L, P	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
C, G, M, Q	IPR009072	Histone-fold	Homologous Superfamily
C, G, M, Q	IPR002119	Histone H2A	Family
C, G, M, Q	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C, G, M, Q	IPR032454	Histone H2A, C-terminal domain	Domain
C, G, M, Q	IPR032458	Histone H2A conserved site	Conserved Site
D, H, N, R	IPR009072	Histone-fold	Homologous Superfamily
D, H, N, R	IPR055333	Histone H2B, conserved site	Conserved Site
D, H, N, R	IPR000558	Histone H2B	Family
D, H, N, R	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
U, V	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
U, V	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
U, V	IPR005818	Linker histone H1/H5, domain H15	Domain
U, V	IPR005819	Linker histone H1/H5	Family