5NBN

Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Actin-like ATPases	8044481	3000092	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Actin-like ATPases	8044482	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8044482	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8044481	3000092	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)
A	PF00022	e5nbnA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00022	ECOD (1.6)
B	PF00022	e5nbnB2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00022	ECOD (1.6)
D	PF00022	e5nbnD2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00022	ECOD (1.6)
C	PF00022	e5nbnC1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00022	ECOD (1.6)
E	PF00022	e5nbnE2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00022	ECOD (1.6)
F	PF00022	e5nbnF2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00022	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
B	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
D	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
C	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
E	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
E	3.30.420.580	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
F	3.30.420.580	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00022	Actin (Actin)	Actin	-	Family
C, D	PF00022	Actin (Actin)	Actin	-	Family
E, F	PF00022	Actin (Actin)	Actin	-	Family
G, H	PF13892	DNA-binding domain (DBINO)	DNA-binding domain	DBINO is a DNA-binding domain found on global transcription activator SNF2L1 proteins and chromatin re-modelling proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Actin-related protein 4	protein binding binding histone binding protein-containing complex binding chromatin binding	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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic 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 organic substance metabolic process organic substance biosynthetic 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 organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly chromosome organization protein-DNA complex assembly cellular component organization cellular component biogenesis protein-DNA complex organization organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cellular component organization or biogenesis centromere complex assembly transcription by RNA polymerase II regulation of transcription by RNA polymerase II chromatin organization chromatin remodeling	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle cellular anatomical entity Ino80 complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen NuA4 histone acetyltransferase complex transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex protein acetyltransferase complex intracellular protein-containing complex histone deacetylase complex nucleoplasm Swr1 complex SWI/SNF complex
C, D	Actin	hydrolase activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding hydrolase activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding structural constituent of cytoskeleton structural molecule activity identical protein binding protein binding	sexual reproduction cellular developmental process reproductive process cellular component assembly involved in morphogenesis cell wall organization or biogenesis cell development cell wall organization spore wall biogenesis developmental process involved in reproduction meiotic cell cycle process ascospore wall assembly cellular component biogenesis cellular component organization cellular anatomical entity morphogenesis cellular component assembly sexual reproduction cellular developmental process reproductive process cellular component assembly involved in morphogenesis cell wall organization or biogenesis cell development cell wall organization spore wall biogenesis developmental process involved in reproduction meiotic cell cycle process ascospore wall assembly cellular component biogenesis cellular component organization cellular anatomical entity morphogenesis cellular component assembly spore wall assembly sexual sporulation cell differentiation anatomical structure development cell cycle cellular component organization or biogenesis cell cycle process developmental process fungal-type cell wall organization cell wall assembly sexual sporulation resulting in formation of a cellular spore reproductive process in single-celled organism meiotic cell cycle ascospore wall biogenesis fungal-type cell wall assembly sporulation resulting in formation of a cellular spore anatomical structure morphogenesis ascospore formation fungal-type cell wall organization or biogenesis cell wall biogenesis anatomical structure formation involved in morphogenesis cellular process sporulation fungal-type cell wall biogenesis external encapsulating structure organization localization import into cell transport endocytosis establishment of localization vesicle-mediated transport establishment of cell polarity establishment or maintenance of cell polarity 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process macromolecule metabolic process cytoskeleton-dependent cytokinesis mitotic cytokinetic process mitotic cytokinesis mitotic actomyosin contractile ring contraction mitotic cell cycle contractile ring contraction cortical actin cytoskeleton organization actin filament-based process actin cytoskeleton organization actomyosin structure organization cortical cytoskeleton organization cytokinesis organelle organization mitotic cell cycle process actomyosin contractile ring contraction cytokinetic process actomyosin contractile ring organization cell division cytoskeleton organization vacuole organization organelle inheritance vacuole inheritance 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 cellular response to stimulus response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair protein localization establishment of protein localization cellular localization nitrogen compound transport secretion organic substance transport establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell protein transport cellular macromolecule localization macromolecule localization protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle cellular anatomical entity Ino80 complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen cell cortex cortical cytoskeleton actin cytoskeleton cell periphery endocytic patch cytoskeleton cortical actin cytoskeleton actin cortical patch cytoplasm NuA4 histone acetyltransferase complex transferase complex H4/H2A histone acetyltransferase complex histone acetyltransferase complex acetyltransferase complex H4 histone acetyltransferase complex protein acetyltransferase complex intracellular protein-containing complex contractile ring cell division site cellular bud neck cellular bud cellular bud neck contractile ring actomyosin contractile ring mitotic actomyosin contractile ring site of polarized growth actin filament bundle histone deacetylase complex nucleoplasm Swr1 complex polymeric cytoskeletal fiber actin filament supramolecular fiber supramolecular polymer supramolecular complex
E, F	Actin-like protein ARP8	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding RNA binding nucleic acid binding mRNA binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination mitotic recombination metabolic process primary metabolic process DNA metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination mitotic recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic 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 regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process DNA repair double-strand break repair protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle cellular anatomical entity Ino80 complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen cytoskeleton cytoplasm
G, H	Putative DNA helicase INO80	protein binding binding histone binding ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding protein binding binding histone binding ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides	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 organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process 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 organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process DNA recombination mitotic recombination telomere organization chromosome organization DNA metabolic process telomere maintenance cellular component organization organelle organization telomere maintenance via recombination cellular component organization or biogenesis DNA duplex unwinding DNA geometric change DNA conformation change regulation of biological process biological regulation regulation of 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 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 subtelomeric heterochromatin formation negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair regulation of transcription by RNA polymerase II TOR signaling regulation of signaling regulation of TOR signaling signaling regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication signal transduction positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle SWI/SNF superfamily-type complex non-membrane-bounded organelle INO80-type complex catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle cellular anatomical entity Ino80 complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR020902	Actin/actin-like conserved site	Conserved Site
A, B	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B	IPR004000	Actin family	Family
C, D	IPR020902	Actin/actin-like conserved site	Conserved Site
C, D	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
C, D	IPR004001	Actin, conserved site	Conserved Site
C, D	IPR004000	Actin family	Family
E, F	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
E, F	IPR004000	Actin family	Family
G, H	IPR000330	SNF2, N-terminal	Domain
G, H	IPR031047	DNA helicase INO80, DEAQ-box helicase domain	Domain
G, H	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
G, H	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
G, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
G, H	IPR001650	Helicase, C-terminal domain-like	Domain
G, H	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
G, H	IPR020838	DBINO domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	HIC	Parent Component: HIS RESID: AA0317 PSI-MOD : 1'-methyl-L-histidine MOD:00322

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.