2XQL | pdb_00002xql

Fitting of the H2A-H2B histones in the electron microscopy map of the complex Nucleoplasmin:H2A-H2B histones (1:5).

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)
J	SCOP2B Superfamily	Core histone-like	8066279	3001387	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Core histone-like	8066279	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8066279	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8066279	3001387	SCOP2B (2022-06-29)
B	SCOP2 Family	Nucleosome core histones	8066278	4000793	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Core histone-like	8066279	3001387	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	Core histone-like	8040591	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8040591	3001387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8040591	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8040591	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8040591	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)
J	Histone	e2xqlJ1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
H	Histone	e2xqlH1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
F	Histone	e2xqlF1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
D	Histone	e2xqlD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
B	Histone	e2xqlB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)
I	Histone_1	e2xqlI1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
G	Histone_1	e2xqlG1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
E	Histone_1	e2xqlE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
C	Histone_1	e2xqlC1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
A	Histone_1	e2xqlA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
A, C, E, G, I	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
A, C, E, G, I	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
B, D, F, H, J	HISTONE H2B 5	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity 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 intracellular membrane-bounded organelle
A, C, E, G, I	HISTONE H2A-IV	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	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
B, D, F, H, J	IPR009072	Histone-fold	Homologous Superfamily
B, D, F, H, J	IPR055333	Histone H2B, conserved site	Conserved Site
B, D, F, H, J	IPR000558	Histone H2B	Family
B, D, F, H, J	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, C, E, G, I	IPR009072	Histone-fold	Homologous Superfamily
A, C, E, G, I	IPR002119	Histone H2A	Family
A, C, E, G, I	IPR032454	Histone H2A, C-terminal domain	Domain
A, C, E, G, I	IPR032458	Histone H2A conserved site	Conserved Site
A, C, E, G, I	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.