9MU4 | pdb_00009mu4

Structure of a native Drosophila melanogaster octameric nucleosome

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
H [auth f]	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2022-06-29)
G [auth b]	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2022-06-29)
F [auth e]	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2022-06-29)
E [auth a]	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2022-06-29)
D [auth h]	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2022-06-29)
C [auth d]	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2022-06-29)
B [auth g]	SCOP2B Superfamily	Core histone-like	8067128	3001387	SCOP2B (2022-06-29)
A [auth c]	SCOP2B Superfamily	Core histone-like	8067128	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)
E [auth a]	ATP-grasp_6	e9mu4a01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: ATP-grasp_6	ECOD (v294.1)
C [auth d]	ATP-grasp_6	e9mu4d01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: ATP-grasp_6	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J [auth N]	DNA (164-MER)	-	-	-
I [auth T]	DNA (164-MER)	-	-	-
G [auth b], H [auth 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 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
E [auth a], F [auth e]	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
C [auth d], D [auth h]	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
A [auth c], B [auth g]	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth b], H [auth f]	IPR009072	Histone-fold	Homologous Superfamily
G [auth b], H [auth f]	IPR035425	CENP-T/Histone H4, histone fold	Domain
G [auth b], H [auth f]	IPR001951	Histone H4	Family
G [auth b], H [auth f]	IPR019809	Histone H4, conserved site	Conserved Site
G [auth b], H [auth f]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
E [auth a], F [auth e]	IPR009072	Histone-fold	Homologous Superfamily
E [auth a], F [auth e]	IPR000164	Histone H3/CENP-A	Family
E [auth a], F [auth e]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C [auth d], D [auth h]	IPR009072	Histone-fold	Homologous Superfamily
C [auth d], D [auth h]	IPR055333	Histone H2B, conserved site	Conserved Site
C [auth d], D [auth h]	IPR000558	Histone H2B	Family
C [auth d], D [auth h]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A [auth c], B [auth g]	IPR009072	Histone-fold	Homologous Superfamily
A [auth c], B [auth g]	IPR002119	Histone H2A	Family
A [auth c], B [auth g]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A [auth c], B [auth g]	IPR032454	Histone H2A, C-terminal domain	Domain
A [auth c], B [auth g]	IPR032458	Histone H2A conserved site	Conserved Site

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.