1ZBB | pdb_00001zbb

Structure of the 4_601_167 Tetranucleosome

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G [auth E]	d1zbbe1	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H3	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
C [auth A]	d1zbba1	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H3	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
D [auth B]	d1zbbb1	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
H [auth F]	d1zbbf1	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
F [auth D]	d1zbbd1	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth E]	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
O [auth e]	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
K [auth a]	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
L [auth b]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
P [auth f]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
J [auth H]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
N [auth d]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
R [auth h]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
M [auth c]	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
Q [auth g]	SCOP2B Superfamily	Core histone-like	8041278	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)
G [auth E]		e1zbbE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
O [auth e]	Sigma_1_2	e1zbbe1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
K [auth a]	Sigma_1_2	e1zbba1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
C [auth A]		e1zbbA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
D [auth B]		e1zbbB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F:	ECOD (v294.1)
H [auth F]	zf-MYND	e1zbbF1	A: a/b three-layered sandwiches	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: zf-MYND	ECOD (v294.1)
L [auth b]	Sigma_1_2	e1zbbb1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
P [auth f]	Sigma_1_2	e1zbbf1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
F [auth D]	Histone	e1zbbD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: Histone	ECOD (v294.1)
J [auth H]	Sigma_1_2	e1zbbH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
N [auth d]	CoV_NSP4_C	e1zbbd2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: CoV_NSP4_C	ECOD (v294.1)
R [auth h]	Sigma_1_2	e1zbbh1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
E [auth C]	Sigma_1_2	e1zbbC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
I [auth G]	Sigma_1_2	e1zbbG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
M [auth c]	Sigma_1_2	e1zbbc1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)
Q [auth g]	Sigma_1_2	e1zbbg1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], G [auth E], K [auth a], O [auth e]	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
D [auth B], H [auth F], L [auth b], P [auth f]	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
E [auth C], I [auth G], M [auth c], Q [auth g]	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
B [auth J]	DNA STRAND 2 (ARBITRARY MODEL SEQUENCE)	-	-	-
C [auth A], G [auth E], K [auth a], O [auth e]	HISTONE H3	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 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
D [auth B], H [auth F], L [auth b], P [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	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
F [auth D], J [auth H], N [auth d], R [auth h]	Histone H2B.1	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
E [auth C], I [auth G], M [auth c], Q [auth g]	Histone H2A.1	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
A [auth I]	DNA STRAND 1 (ARBITRARY MODEL SEQUENCE)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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