2ACJ | pdb_00002acj

Crystal structure of the B/Z junction containing DNA bound to Z-DNA binding proteins

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth D]	d2acjd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Z-DNA binding domain	Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth D]	d2acjd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d2acjc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Z-DNA binding domain	Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth C]	d2acjc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d2acjb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Z-DNA binding domain	Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d2acjb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d2acja1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Z-DNA binding domain	Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d2acja2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth D]	SCOP2B Superfamily	Winged helix DNA-binding domain	8057679	3000034	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Winged helix DNA-binding domain	8057679	3000034	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Winged helix DNA-binding domain	8057679	3000034	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)
F [auth D]	Pox_D5	e2acjD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pox_D5	ECOD (v294.1)
E [auth C]	Pox_D5	e2acjC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pox_D5	ECOD (v294.1)
D [auth B]	Pox_D5	e2acjB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pox_D5	ECOD (v294.1)
C [auth A]	Pox_D5	e2acjA1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pox_D5	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth D]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E [auth C]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D [auth B]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C [auth A]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B], E [auth C], F [auth D]	PF02295	Adenosine deaminase z-alpha domain (z-alpha)	Adenosine deaminase z-alpha domain	This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to ...	This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E]	5'-D(GPTPCPGPCPGPCPGPCPCPAPTPAPAPAPCP*C)-3'	-	-	-
B [auth F]	5'-D(APCPGPGPTPTPTPAPTPGPGPCPGPCPGPCP*G)-3'	-	-	-
C [auth A], D [auth B], E [auth C], F [auth D]	Double-stranded RNA-specific adenosine deaminase	RNA binding double-stranded RNA binding binding nucleic acid binding DNA binding double-stranded RNA adenosine deaminase activity hydrolase activity deaminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines adenosine deaminase activity tRNA-specific adenosine deaminase activity catalytic activity, acting on RNA RNA binding double-stranded RNA binding binding nucleic acid binding DNA binding double-stranded RNA adenosine deaminase activity hydrolase activity deaminase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines adenosine deaminase activity tRNA-specific adenosine deaminase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA cation binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA modification adenosine to inosine editing base conversion or substitution editing macromolecule modification metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process positive regulation of biological process RNA metabolic process primary metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA modification adenosine to inosine editing base conversion or substitution editing macromolecule modification metabolic process cellular process macromolecule metabolic process regulation of cellular process negative regulation of biological process positive regulation of biological process positive regulation of macromolecule biosynthetic process post-transcriptional regulation of gene expression positive regulation of metabolic process negative regulation of post-transcriptional gene silencing by regulatory ncRNA regulation of gene silencing by regulatory ncRNA positive regulation of biosynthetic process negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of macromolecule metabolic process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process negative regulation of gene silencing by regulatory ncRNA biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of gene expression negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing regulation of macromolecule biosynthetic process negative regulation of post-transcriptional gene silencing regulation of metabolic process immune system development developmental process multicellular organism development multicellular organismal process immune system process somatic diversification of immune receptors via somatic mutation anatomical structure development somatic diversification of immune receptors system development regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of catalytic activity regulation of transferase activity regulation of primary metabolic process negative regulation of kinase activity phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation negative regulation of protein kinase activity by regulation of protein phosphorylation regulation of protein metabolic process negative regulation of molecular function negative regulation of protein kinase activity regulation of protein kinase activity regulation of molecular function regulation of kinase activity negative regulation of protein phosphorylation negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation cellular developmental process ossification cell differentiation osteoblast differentiation cellular localization establishment of protein localization nucleocytoplasmic transport transport nuclear transport intracellular transport protein export from nucleus establishment of localization localization protein transport establishment of localization in cell macromolecule localization intracellular protein localization nuclear export intracellular protein transport mRNA modification mRNA metabolic process cellular response to stimulus response to stimulus regulation of type I interferon-mediated signaling pathway response to cytokine regulation of signal transduction response to biotic stimulus cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus regulation of immune system process signal transduction immune response response to other organism regulation of innate immune response negative regulation of immune response response to external stimulus regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus response to chemical defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response response to type I interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling signaling negative regulation of cell communication cytokine-mediated signaling pathway response to stress regulation of response to stress innate immune response response to external biotic stimulus regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus defense response regulation of cytokine-mediated signaling pathway defense response to symbiont negative regulation of signal transduction response to peptide negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway type I interferon-mediated signaling pathway regulation of cell communication negative regulation of type I interferon-mediated signaling pathway negative regulation of innate immune response pre-miRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA processing nucleobase-containing compound biosynthetic process regulatory ncRNA processing miRNA processing protein localization to nucleus import into nucleus establishment of protein localization to organelle protein localization to organelle protein import into nucleus negative regulation of hepatocyte apoptotic process regulation of epithelial cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death epithelial cell apoptotic process negative regulation of apoptotic process regulation of hepatocyte apoptotic process negative regulation of epithelial cell apoptotic process hepatocyte apoptotic process apoptotic process programmed cell death mRNA processing ribonucleoprotein complex biogenesis RISC complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization positive regulation of viral genome replication positive regulation of viral process viral life cycle regulation of viral life cycle regulation of viral process viral genome replication viral process regulation of viral genome replication multicellular organismal-level homeostasis homeostatic process hematopoietic stem cell homeostasis homeostasis of number of cells hemopoiesis cell development erythrocyte differentiation myeloid cell differentiation myeloid cell homeostasis erythrocyte homeostasis response to virus definitive hemopoiesis response to interferon-alpha hematopoietic progenitor cell differentiation defense response to virus cellular response to virus	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen membrane cytosol protein-containing complex nuclear protein-containing complex supraspliceosomal complex spliceosomal complex ribonucleoprotein complex nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B], E [auth C], F [auth D]	IPR044456	ADAR1, first double-stranded RNA binding domain	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	IPR002466	Adenosine deaminase/editase	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	IPR042371	Z-binding domain	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C [auth A], D [auth B], E [auth C], F [auth D]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
C [auth A], D [auth B], E [auth C], F [auth D]	IPR044457	ADAR1, third double-stranded RNA binding domain	Domain
C [auth A], D [auth B], E [auth C], F [auth D]	IPR014720	Double-stranded RNA-binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A], D [auth B], E [auth C], F [auth D]	Pharos: P55265	Aicardi-Goutieres syndrome dyschromatosis symmetrica hereditaria Aicardi-Goutieres syndrome 6 breast carcinoma ovarian cancer pseudo-TORCH syndrome Duchenne muscular dystrophy familial infantile bilateral striatal necrosis juvenile dermatomyositis Mammary Neoplasms pancreatic intraductal papillary-mucinous neoplasm Aicardi-Goutieres syndrome 1 astrocytic tumor cutaneous lupus erythematosus infantile bilateral striatal necrosis Aicardi-Goutieres syndrome dyschromatosis symmetrica hereditaria Aicardi-Goutieres syndrome 6 breast carcinoma ovarian cancer pseudo-TORCH syndrome Duchenne muscular dystrophy familial infantile bilateral striatal necrosis juvenile dermatomyositis Mammary Neoplasms pancreatic intraductal papillary-mucinous neoplasm Aicardi-Goutieres syndrome 1 astrocytic tumor cutaneous lupus erythematosus infantile bilateral striatal necrosis leukodystrophy plasma cell myeloma Aicardi-Goutieres syndrome 2 breast cancer dermatomyositis intellectual disability

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.