3RNU | pdb_00003rnu

Structural Basis of Cytosolic DNA Sensing by Innate Immune Receptors

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
D	d3rnud1	All beta proteins	OB-fold	HIN-2000 domain-like	HIN-200/IF120x domain	Gamma-interferon-inducible protein Ifi-16	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3rnud3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3rnuc1	All beta proteins	OB-fold	HIN-2000 domain-like	HIN-200/IF120x domain	Gamma-interferon-inducible protein Ifi-16	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3rnuc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rnub1	All beta proteins	OB-fold	HIN-2000 domain-like	HIN-200/IF120x domain	Gamma-interferon-inducible protein Ifi-16	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rnub4	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rnub3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3rnua1	All beta proteins	OB-fold	HIN-2000 domain-like	HIN-200/IF120x domain	Gamma-interferon-inducible protein Ifi-16	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3rnua3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	RPA43_OB	e3rnuD3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
C	RPA43_OB	e3rnuC3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
B	RPA43_OB	e3rnuB3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)
A	RPA43_OB	e3rnuA3	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: RPA43_OB	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02760	HIN-200/IF120x domain (HIN)	HIN-200/IF120x domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Gamma-interferon-inducible protein 16	RNA binding binding nucleic acid binding transcription factor binding protein binding DNA binding double-stranded DNA binding identical protein binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus positive regulation of immune system process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cellular response to stimulus signaling signal transduction by p53 class mediator cell death intracellular signal transduction cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death cellular response to nutrient levels response to nutrient levels cellular response to stress response to starvation cellular response to glucose starvation cellular response to starvation catabolic process autophagy process utilizing autophagic mechanism negative regulation of response to biotic stimulus negative regulation of response to stimulus negative regulation of immune response negative regulation of immune system process negative regulation of response to external stimulus negative regulation of defense response negative regulation of innate immune response response to ionizing radiation cellular response to ionizing radiation response to radiation response to abiotic stimulus cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus pattern recognition receptor signaling pathway regulation of signal transduction cellular component biogenesis immune response-activating signaling pathway cellular component assembly inflammasome-mediated signaling pathway innate immune response-activating signaling pathway negative regulation of cellular component organization regulation of inflammasome-mediated signaling pathway negative regulation of protein-containing complex assembly regulation of pattern recognition receptor signaling pathway inflammatory response cytoplasmic pattern recognition receptor signaling pathway regulation of cellular component organization intracellular receptor signaling pathway negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction AIM2 inflammasome complex assembly regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication cellular component organization regulation of protein-containing complex assembly immune response-regulating signaling pathway regulation of intracellular signal transduction protein-containing complex assembly negative regulation of AIM2 inflammasome complex assembly cellular component organization or biogenesis regulation of signaling protein-containing complex organization regulation of cellular component biogenesis negative regulation of signal transduction regulation of AIM2 inflammasome complex assembly regulation of cell communication negative regulation of inflammasome-mediated signaling pathway cellular response to interferon-beta response to peptide response to interferon-beta response to chemical response to cytokine cellular response to cytokine stimulus chromatin organization chromatin remodeling epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic multicellular organismal process interleukin-1 production regulation of interleukin-1 beta production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of interleukin-1 beta production positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of interleukin-1 production interleukin-1 beta production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production regulation of inflammatory response developmental process myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development mononuclear cell differentiation myeloid cell differentiation cell differentiation anatomical structure development monocyte differentiation leukocyte differentiation negative regulation of viral genome replication viral life cycle negative regulation of viral process regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication regulation of molecular function regulation of DNA binding regulation of binding negative regulation of binding negative regulation of molecular function negative regulation of DNA binding intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator DNA damage response intrinsic apoptotic signaling pathway in response to DNA damage regulation of catabolic process regulation of autophagy transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II defense response to virus response to virus positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule cytoplasm cytosol
F [auth L]	DNA (5'-D(TPCPTPCPTPCPTPTPTPGPAPTPGPGPCPC)-3')	-	-	-
E [auth K]	DNA (5'-D(GPCPCPAPTPCPAPAPAPGPAPGPAPGPAPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004021	HIN-200/IF120x	Domain
A, B, C, D	IPR040205	HIN-200 family	Family
A, B, C, D	IPR004020	DAPIN domain	Domain
A, B, C, D	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q16666	psoriasis lymphoplasmacytic lymphoma malignant pancreatic neoplasm myopathy osteosarcoma adenoma pancreatic intraductal papillary-mucinous neoplasm breast cancer pilocytic astrocytoma cystic fibrosis Down syndrome systemic lupus erythematosus gastric carcinoma large cell medulloblastoma lung cancer psoriasis lymphoplasmacytic lymphoma malignant pancreatic neoplasm myopathy osteosarcoma adenoma pancreatic intraductal papillary-mucinous neoplasm breast cancer pilocytic astrocytoma cystic fibrosis Down syndrome systemic lupus erythematosus gastric carcinoma large cell medulloblastoma lung cancer malignant ependymoma medulloblastoma nephrosclerosis ovarian cancer astrocytic tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Crohn disease plasma cell myeloma dermatomyositis Sjogren syndrome Duchenne muscular dystrophy ulcerative colitis glioblastoma limb-girdle muscular dystrophy lung carcinoma malignant glioma multiple sclerosis oligodendroglioma pancreatic ductal adenocarcinoma Becker muscular dystrophy Pick disease cutaneous lupus erythematosus primitive neuroectodermal tumor diabetes mellitus subependymal giant cell astrocytoma Emery-Dreifuss muscular dystrophy juvenile dermatomyositis lung adenocarcinoma

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.