Annotations: 23IL

Cryo-EM structure of Chaetomium thermophilum SWI/SNF bound to a nucleosome

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 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
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
D, 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 antibacterial humoral response defense response to bacterium response to bacterium cellular component organization chromatin organization cellular process cellular component organization or biogenesis	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
I [auth K]	WD40 repeat-containing protein	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 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 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 protein binding histone binding hydrolase activity	regulation of cellular 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 biological regulation primary metabolic process regulation of cellular 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 biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process transcription by RNA polymerase II cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
J [auth L]	Putative chromatin structure remodeling complex protein	-	-	-
K [auth M]	Actin-related protein 4	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 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	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 cellular process macromolecule metabolic process DNA repair RNA metabolic process 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 cellular process macromolecule metabolic process DNA repair RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process cellular component organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
L [auth N], M [auth O]	Ssr1	DNA binding binding nucleic acid binding protein binding histone binding	regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process 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 positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle SWI/SNF complex ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure membrane-bounded organelle SWI/SNF complex ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle membraneless organelle SWI/SNF superfamily-type complex
N [auth P]	DM2 domain-containing protein	-	-	-
O [auth Q]	DUF1750-domain-containing protein	-	cellular component organization chromatin organization chromatin remodeling cellular process cellular component organization or biogenesis	-
P [auth R]	ARID domain-containing protein	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	regulation of cellular 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process regulation of cellular 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process 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 regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	membrane-bounded organelle SWI/SNF complex ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure membrane-bounded organelle SWI/SNF complex ATPase complex protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle membraneless organelle SWI/SNF superfamily-type complex
Q [auth S]	Snf5	-	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 metabolic process cellular process macromolecule 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 metabolic process cellular process macromolecule metabolic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen
R [auth T]	Nuclear localization protein	DNA binding binding chromatin binding nucleic acid binding chromatin DNA binding	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 metabolic process cellular process macromolecule metabolic process	RSC-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 intracellular organelle cellular anatomical structure RSC-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 intracellular organelle cellular anatomical structure organelle membraneless organelle SWI/SNF superfamily-type complex
S [auth U]	LYR family protein	-	-	-
T [auth I]	DNA (167-MER)	-	-	-
U [auth J]	DNA (167-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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
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
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
I [auth K]	IPR019775	WD40 repeat, conserved site	Conserved Site
I [auth K]	IPR001650	Helicase, C-terminal domain-like	Domain
I [auth K]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
I [auth K]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
I [auth K]	IPR001487	Bromodomain	Domain
I [auth K]	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
I [auth K]	IPR001680	WD40 repeat	Repeat
I [auth K]	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
I [auth K]	IPR014012	Helicase/SANT-associated domain	Domain
I [auth K]	IPR014978	Glutamine-Leucine-Glutamine, QLQ	Domain
I [auth K]	IPR029295	Snf2, ATP coupling domain	Domain
I [auth K]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
I [auth K]	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
I [auth K]	IPR000330	SNF2, N-terminal domain	Domain
I [auth K]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
J [auth L]	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
J [auth L]	IPR035959	RutC-like superfamily	Homologous Superfamily
J [auth L]	IPR006175	YjgF/YER057c/UK114 family	Family
J [auth L]	IPR004000	Actin family	Family
K [auth M]	IPR004001	Actin, conserved site	Conserved Site
K [auth M]	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
K [auth M]	IPR004000	Actin family	Family
L [auth N], M [auth O]	IPR009057	Homeodomain-like superfamily	Homologous Superfamily
L [auth N], M [auth O]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
L [auth N], M [auth O]	IPR017884	SANT domain	Domain
L [auth N], M [auth O]	IPR001005	SANT/Myb domain	Domain
L [auth N], M [auth O]	IPR007526	SWIRM domain	Domain
L [auth N], M [auth O]	IPR032451	SMARCC, C-terminal	Domain
L [auth N], M [auth O]	IPR041984	Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type	Domain
N [auth P]	IPR003121	SWIB/MDM2 domain	Domain
N [auth P]	IPR036885	SWIB/MDM2 domain superfamily	Homologous Superfamily
N [auth P]	IPR019835	SWIB domain	Domain
O [auth Q]	IPR013859	SWI/SNF and RSC complexes subunit Ssr4, N-terminal	Domain
O [auth Q]	IPR046464	SWI/SNF and RSC complexes subunit Ssr4, C-terminal	Domain
P [auth R]	IPR051232	ARID/SWI1_ChromRemod	Unknown
P [auth R]	IPR001606	ARID DNA-binding domain	Domain
P [auth R]	IPR036431	ARID DNA-binding domain superfamily	Homologous Superfamily
Q [auth S]	IPR006939	SNF5/SMARCB1/INI1	Family
R [auth T]	IPR013933	Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82	Family

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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.

23IL | pdb_000023il

Cryo-EM structure of Chaetomium thermophilum SWI/SNF bound to a nucleosome

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage