Annotations: 7X3X

Cryo-EM structure of N1 nucleosome-RA

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)
H	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8041279	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8041278	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8042439	3001387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8041272	3001387	SCOP2B (2022-06-29)
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)
K [auth V]	AAA_6	e7x3xV1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_6	ECOD (v295)
H	Serpin	e7x3xH1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Serpin	ECOD (v295)
D	Serpin	e7x3xD1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Serpin	ECOD (v295)
G	Serpin	e7x3xG1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Serpin	ECOD (v295)
C	Serpin	e7x3xC1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Serpin	ECOD (v295)
F	Serpin	e7x3xF1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Serpin	ECOD (v295)
B	Serpin	e7x3xB1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Serpin	ECOD (v295)
E	Serpin	e7x3xE1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Serpin	ECOD (v295)
A	Serpin	e7x3xA1	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Serpin	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, G	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
B, 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
A, 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
K [auth V]	ISWI chromatin-remodeling complex ATPase ISW1	nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding hydrolase activity mRNA 3'-UTR binding RNA binding mRNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding rDNA binding ATP-dependent activity, acting on DNA nucleosome array spacer activity ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA histone octamer slider activity protein-containing complex binding nucleosome binding	regulation of cellular process RNA metabolic process regulation of transcriptional start site selection at RNA polymerase II promoter regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of DNA-templated transcription initiation regulation of RNA metabolic process DNA-templated transcriptional start site selection transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of transcription, start site selection regulation of cellular process RNA metabolic process regulation of transcriptional start site selection at RNA polymerase II promoter regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of DNA-templated transcription initiation regulation of RNA metabolic process DNA-templated transcriptional start site selection transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of transcription, start site selection transcription initiation at RNA polymerase II promoter regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process regulation of transcription initiation by RNA polymerase II cellular process metabolic process regulation of macromolecule biosynthetic process transcriptional start site selection at RNA polymerase II promoter regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process DNA-templated transcription termination termination of RNA polymerase II transcription cellular component organization organelle organization chromosome organization sister chromatid cohesion cellular component organization or biogenesis cell cycle cell cycle process regulation of chromatin organization regulation of cellular component organization chromatin organization transcription by RNA polymerase I termination of RNA polymerase I transcription regulation of localization negative regulation of RNA export from nucleus cellular localization negative regulation of nucleocytoplasmic transport nitrogen compound transport nucleocytoplasmic transport transport nuclear transport negative regulation of biological process negative regulation of transport localization intercellular transport establishment of localization in cell negative regulation of cellular process RNA localization nuclear export nucleobase-containing compound transport regulation of intracellular transport negative regulation of intracellular transport RNA transport regulation of transport negative regulation of nucleobase-containing compound transport regulation of nucleobase-containing compound transport regulation of RNA export from nucleus nucleic acid transport intracellular transport regulation of nucleocytoplasmic transport establishment of localization RNA export from nucleus establishment of RNA localization regulation of cellular localization macromolecule localization DNA-templated transcription elongation cellular component biogenesis cellular component assembly chromatin remodeling negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of cellular response to stress endoplasmic reticulum unfolded protein response regulation of response to endoplasmic reticulum stress regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of endoplasmic reticulum unfolded protein response cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress signal transduction negative regulation of IRE1-mediated unfolded protein response response to endoplasmic reticulum stress regulation of IRE1-mediated unfolded protein response negative regulation of endoplasmic reticulum unfolded protein response negative regulation of response to endoplasmic reticulum stress regulation of signaling cellular response to topologically incorrect protein negative regulation of response to stimulus cellular response to unfolded protein response to unfolded protein negative regulation of signal transduction regulation of response to stimulus response to topologically incorrect protein IRE1-mediated unfolded protein response regulation of cell communication response to heat response to abiotic stimulus response to temperature stimulus positive regulation of DNA-templated transcription positive regulation of biological 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 cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle Isw1a complex intracellular organelle ISWI-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle Isw1a complex intracellular organelle ISWI-type complex cellular anatomical structure organelle membraneless organelle Isw1 complex SWI/SNF superfamily-type complex nucleolar chromatin membrane-enclosed lumen nuclear chromosome nucleolus intracellular organelle lumen organelle lumen nuclear lumen Isw1b complex
J	DNA (146-MER)	-	-	-
I	DNA (146-MER)	-	-	-
D, H	Histone H2B 1.1	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
C, 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
B, 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
A, 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
K [auth V]	IPR009057	Homeodomain-like superfamily	Homologous Superfamily
K [auth V]	IPR015195	SLIDE domain	Domain
K [auth V]	IPR036306	ISWI, HAND domain superfamily	Homologous Superfamily
K [auth V]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
K [auth V]	IPR015194	ISWI, HAND domain	Domain
K [auth V]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
K [auth V]	IPR000330	SNF2, N-terminal domain	Domain
K [auth V]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
K [auth V]	IPR001650	Helicase, C-terminal domain-like	Domain
K [auth V]	IPR044754	Isw1/2, N-terminal	Domain
K [auth V]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
K [auth V]	IPR017884	SANT domain	Domain
K [auth V]	IPR001005	SANT/Myb domain	Domain
D, H	IPR009072	Histone-fold	Homologous Superfamily
D, H	IPR000558	Histone H2B	Family
D, H	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
D, H	IPR055333	Histone H2B, conserved site	Conserved Site
C, G	IPR009072	Histone-fold	Homologous Superfamily
C, G	IPR002119	Histone H2A	Family
C, G	IPR032454	Histone H2A, C-terminal domain	Domain
C, G	IPR032458	Histone H2A conserved site	Conserved Site
C, G	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B, F	IPR009072	Histone-fold	Homologous Superfamily
B, F	IPR001951	Histone H4	Family
B, F	IPR035425	CENP-T/Histone H4, histone fold	Domain
B, F	IPR019809	Histone H4, conserved site	Conserved Site
B, F	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
A, E	IPR009072	Histone-fold	Homologous Superfamily
A, E	IPR000164	Histone H3/CENP-A	Family
A, E	IPR007125	Core Histone H2A/H2B/H3 domain	Domain