1P3I | pdb_00001p3i

Crystallographic Studies of Nucleosome Core Particles containing Histone 'Sin' Mutants

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
J [auth H]	d1p3ih_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
F [auth D]	d1p3id_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
I [auth G]	d1p3ig_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2A	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
E [auth C]	d1p3ic_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2A	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
H [auth F]	d1p3if_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
D [auth B]	d1p3ib_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
G [auth E]	d1p3ie_	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]	d1p3ia_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H3	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)
J [auth H]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
G [auth E]	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J [auth H]	TFIID_20kDa	e1p3iH1	A: alpha arrays	X: Urease, gamma-subunit	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: TFIID_20kDa	ECOD (v295)
F [auth D]	TFIID_20kDa	e1p3iD1	A: alpha arrays	X: Urease, gamma-subunit	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: TFIID_20kDa	ECOD (v295)
I [auth G]	TFIID_20kDa	e1p3iG1	A: alpha arrays	X: Urease, gamma-subunit	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: TFIID_20kDa	ECOD (v295)
E [auth C]	TFIID_20kDa	e1p3iC1	A: alpha arrays	X: Urease, gamma-subunit	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: TFIID_20kDa	ECOD (v295)
H [auth F]	TFIID_20kDa	e1p3iF1	A: alpha arrays	X: Urease, gamma-subunit	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: TFIID_20kDa	ECOD (v295)
D [auth B]	TFIID_20kDa	e1p3iB1	A: alpha arrays	X: Urease, gamma-subunit	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: TFIID_20kDa	ECOD (v295)
G [auth E]	TFIID_20kDa	e1p3iE1	A: alpha arrays	X: Urease, gamma-subunit	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: TFIID_20kDa	ECOD (v295)
C [auth A]	TFIID_20kDa	e1p3iA1	A: alpha arrays	X: Urease, gamma-subunit	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: TFIID_20kDa	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth H]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
F [auth D]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
I [auth G]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
E [auth C]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
H [auth F]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
D [auth B]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
G [auth E]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
C [auth A]	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth C], I [auth G]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
C [auth A], G [auth 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
F [auth D], J [auth H]	Histone H2B	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	biological process involved in interspecies interaction between organisms innate immune response in mucosa response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus biological process involved in interspecies interaction between organisms innate immune response in mucosa response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus mucosal immune response organ or tissue specific immune response humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide 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 antibacterial humoral response defense response to bacterium response to bacterium	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]	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	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
D [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 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	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
C [auth A], G [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	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 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
A [auth I], B [auth J]	Palindromic 146bp Human Alpha-Satellite DNA fragment	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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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.