1ID3

CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS

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)
C [auth A]	d1id3a_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H3	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G [auth E]	d1id3e_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H3	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D [auth B]	d1id3b_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H [auth F]	d1id3f_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H4	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E [auth C]	d1id3c_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2A	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
I [auth G]	d1id3g_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2A	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F [auth D]	d1id3d_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
J [auth H]	d1id3h_	All alpha proteins	Histone-fold	Histone-fold	Nucleosome core histones	Histone H2B	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2 Family	Nucleosome core histones	8024206	4000793	SCOP2 (2021-05-27)
C [auth A]	SCOP2 Superfamily	Core histone-like	8036585	3001387	SCOP2 (2021-05-27)
G [auth E]	SCOP2B Superfamily	Core histone-like	8036585	3001387	SCOP2B (2021-05-27)
D [auth B]	SCOP2 Family	Nucleosome core histones	8024207	4000793	SCOP2 (2021-05-27)
D [auth B]	SCOP2 Superfamily	Core histone-like	8036586	3001387	SCOP2 (2021-05-27)
H [auth F]	SCOP2B Superfamily	Core histone-like	8036586	3001387	SCOP2B (2021-05-27)
E [auth C]	SCOP2 Family	Nucleosome core histones	8024209	4000793	SCOP2 (2021-05-27)
E [auth C]	SCOP2 Superfamily	Core histone-like	8036588	3001387	SCOP2 (2021-05-27)
I [auth G]	SCOP2B Superfamily	Core histone-like	8036588	3001387	SCOP2B (2021-05-27)
F [auth D]	SCOP2 Family	Nucleosome core histones	8024211	4000793	SCOP2 (2021-05-27)
F [auth D]	SCOP2 Superfamily	Core histone-like	8036590	3001387	SCOP2 (2021-05-27)
J [auth H]	SCOP2B Superfamily	Core histone-like	8036590	3001387	SCOP2B (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth A]	PF00125	e1id3A1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
G [auth E]	PF00125	e1id3E1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
D [auth B]	PF15511	e1id3B1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
H [auth F]	PF15511	e1id3F1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF15511	ECOD (1.6)
E [auth C]	PF00125,PF16211	e1id3C1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
I [auth G]	PF00125,PF16211	e1id3G1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125,PF16211	ECOD (1.6)
F [auth D]	PF00125	e1id3D1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)
J [auth H]	PF00125	e1id3H1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: PF00125	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth I], B [auth J]	PALINDROMIC 146BP DNA FRAGMENT	-	-	-
C [auth A], G [auth E]	HISTONE H3	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	nucleolar large rRNA transcription by RNA polymerase I cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I nucleolar large rRNA transcription by RNA polymerase I cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process developmental process sexual sporulation resulting in formation of a cellular spore sexual reproduction reproductive process meiotic cell cycle developmental process involved in reproduction sporulation resulting in formation of a cellular spore anatomical structure morphogenesis sexual sporulation anatomical structure formation involved in morphogenesis anatomical structure development sporulation cell cycle cellular response to stimulus global genome nucleotide-excision repair response to stimulus DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle replication fork protection complex nuclear replication fork nuclear chromosome chromosome replication fork CENP-A containing chromatin protein-DNA complex nucleosome chromatin chromosomal region chromosome, centromeric core domain CENP-A containing nucleosome chromosome, centromeric region
D [auth B], H [auth F]	HISTONE H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	nucleolar large rRNA transcription by RNA polymerase I cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I nucleolar large rRNA transcription by RNA polymerase I cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle replication fork protection complex nuclear replication fork nuclear chromosome chromosome replication fork protein-DNA complex nucleosome chromatin
E [auth C], I [auth G]	HISTONE H2A.1	DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin 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-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular process heterochromatin organization cellular component organization or biogenesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular process heterochromatin organization cellular component organization or biogenesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process	membrane-bounded organelle replication fork protection complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear replication fork nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle membrane-bounded organelle replication fork protection complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear replication fork nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle replication fork non-membrane-bounded organelle nuclear lumen protein-DNA complex nucleosome chromatin
F [auth D], J [auth H]	HISTONE H2B.2	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle replication fork protection complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear replication fork nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle membrane-bounded organelle replication fork protection complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear replication fork nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle replication fork non-membrane-bounded organelle nuclear lumen protein-DNA complex nucleosome chromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], G [auth E]	IPR009072	Histone-fold	Homologous Superfamily
C [auth A], G [auth E]	IPR007125	Histone H2A/H2B/H3	Domain
C [auth A], G [auth E]	IPR000164	Histone H3/CENP-A	Family
D [auth B], H [auth F]	IPR009072	Histone-fold	Homologous Superfamily
D [auth B], H [auth F]	IPR035425	CENP-T/Histone H4, histone fold	Domain
D [auth B], H [auth F]	IPR001951	Histone H4	Family
D [auth B], H [auth F]	IPR019809	Histone H4, conserved site	Conserved Site
E [auth C], I [auth G]	IPR009072	Histone-fold	Homologous Superfamily
E [auth C], I [auth G]	IPR007125	Histone H2A/H2B/H3	Domain
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
F [auth D], J [auth H]	IPR009072	Histone-fold	Homologous Superfamily
F [auth D], J [auth H]	IPR007125	Histone H2A/H2B/H3	Domain
F [auth D], J [auth H]	IPR000558	Histone H2B	Family

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 R01GM133198.