8COM | pdb_00008com

Structure of the Nucleosome Core Particle from Trypanosoma brucei

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	Histone	e8comH1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Histone	ECOD (develop294)
D	V-set	e8comD1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: V-set	ECOD (develop294)
G	V-set	e8comG1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: V-set	ECOD (develop294)
C	Histone	e8comC1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Histone	ECOD (develop294)
F	Histone	e8comF1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Histone	ECOD (develop294)
B	V-set	e8comB1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: V-set	ECOD (develop294)
E	Histone	e8comE1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Histone	ECOD (develop294)
A	V-set	e8comA1	A: alpha bundles	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: V-set	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, G	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
A, E	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J	Widom 601 145 bp DNA (127-mer ordered and built)	-	-	-
I	Widom 601 145 bp DNA (127-mer ordered and built)	-	-	-
D, H	Histone H2B	DNA binding binding nucleic acid binding ion binding anion binding phosphate ion binding small molecule 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 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 organization	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
C, G	Histone H2A	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity 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 organelle organization chromosome organization	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
B, F	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 cell projection cellular anatomical structure intracellular anatomical structure ciliary plasm organelle cilium cytoplasm plasma membrane bounded cell projection ciliary transition zone nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen membrane-bounded organelle cell projection cellular anatomical structure intracellular anatomical structure ciliary plasm organelle cilium cytoplasm plasma membrane bounded cell projection ciliary transition zone nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen nuclear lumen protein-containing complex protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome membraneless organelle nucleoplasm
A, E	Histone H3, putative	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity ion binding anion binding phosphate ion binding small molecule binding structural molecule activity structural constituent of chromatin	-	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, H	IPR009072	Histone-fold	Homologous Superfamily
D, H	IPR000558	Histone H2B	Family
D, H	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
D, H	IPR055333	Histone H2B, conserved site	Conserved Site
C, G	IPR009072	Histone-fold	Homologous Superfamily
C, G	IPR002119	Histone H2A	Family
C, G	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C, G	IPR032454	Histone H2A, C-terminal domain	Domain
C, G	IPR032458	Histone H2A conserved site	Conserved Site
B, F	IPR009072	Histone-fold	Homologous Superfamily
B, F	IPR001951	Histone H4	Family
A, E	IPR009072	Histone-fold	Homologous Superfamily
A, E	IPR000164	Histone H3/CENP-A	Family
A, E	IPR007125	Core Histone H2A/H2B/H3 domain	Domain

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.