4A36 | pdb_00004a36

Structure of duck RIG-I helicase domain bound to 19-mer dsRNA and ATP transition state analogue

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8092829	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8092828	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8092829	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8092828	3002019	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)
B	MDA5_ID	e4a36B4	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: MDA5_ID	ECOD (1.6)
B	DEAD_1	e4a36B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
B	Helicase_C_1	e4a36B3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_1	ECOD (1.6)
A	MDA5_ID	e4a36A3	A: alpha bundles	X: Helical bundle insertion in helicase domains	H: Helical bundle in Hef helicase (From Topology)	T: Helical bundle in Hef helicase	F: MDA5_ID	ECOD (1.6)
A	DEAD_1	e4a36A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
A	Helicase_C_1	e4a36A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
B	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (4.2.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.2.0)
A	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth R], E [auth T]	5'-R(GPCPAPUPGPCPGPAPCPCPUPCPUPGP UPUPUPGP*A)-3'	-	-	-
D [auth S], F [auth U]	5'-R(UPCPAPAPAPCPAPGPAPGPGPUPCPGP CPAPUPGP*C)-3'	-	-	-
A, B	RETINOIC ACID INDUCIBLE PROTEIN I	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 RNA binding double-stranded RNA binding nucleic acid binding hydrolase activity catalytic activity single-stranded RNA binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity cation binding transition metal ion binding zinc ion binding metal ion binding	cellular response to stimulus cytoplasmic pattern recognition receptor signaling pathway 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 regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus intracellular signal transduction cellular response to stimulus cytoplasmic pattern recognition receptor signaling pathway 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 regulation of cellular process pattern recognition receptor signaling pathway response to stimulus regulation of response to external stimulus intracellular receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus intracellular signal transduction cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway 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 signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response biological regulation 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 cellular process activation of immune response defense response to virus antiviral innate immune response response to virus	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR038557	RIG-I-like receptor, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR021673	RIG-I-like receptor, C-terminal regulatory domain	Domain
A, B	IPR031964	Caspase recruitment domain	Domain
A, B	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B	IPR001650	Helicase, C-terminal domain-like	Domain
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR042145	RIG-I, CARD domain repeat 2	Domain
A, B	IPR051363	RIG-I-like Receptor (RLR) Helicase	Family
A, B	IPR041204	RIG-I-like receptor, C-terminal	Domain
A, B	IPR011545	DEAD/DEAH-box helicase domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.