5JCF | pdb_00005jcf

Crystal structure of chicken MDA5 with 5'p 10-mer dsRNA and ADP-Mg2+ at 2.6 A resolution (orthorhombic form).

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)
D [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103692	3002019	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Mss4-like	8103690	3001994	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8103693	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8103692	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8103693	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mss4-like	8103690	3001994	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)
D [auth B]	RIG-I_C-RD	e5jcfB1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: RIG-I_C-RD	ECOD (1.6)
D [auth B]	MDA5_ID	e5jcfB5	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)
D [auth B]	DEAD_1	e5jcfB3	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)
D [auth B]	Helicase_C_1	e5jcfB4	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	RIG-I_C-RD	e5jcfA1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: RIG-I_C-RD	ECOD (1.6)
A	MDA5_ID	e5jcfA4	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	e5jcfA2	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	e5jcfA3	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)
D [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
D [auth B]	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (utative)
D [auth B]	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (utative)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	1.20.1320.30	Mainly Alpha	Up-down Bundle	phosphoenolpyruvate carboxylase, domain 3		CATH (utative)
A	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth Y]	RNA (5'-R(PAPGPGPUPAPCPGPUPAPCP*C)-3')	-	-	-
B [auth X], E [auth C], F [auth D]	RNA (5'-R(PGPGPUPAPCPGPUPAPCPC)-3')	-	-	-
A, D [auth B]	Melanoma differentiation associated protein-5	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 DNA binding nucleic acid binding hydrolase activity catalytic activity 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 RNA binding cation binding metal ion binding	biological process involved in interspecies interaction between organisms 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 defense response to virus biological process involved in interspecies interaction between organisms 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 defense response to virus response to virus	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR038557	RIG-I-like receptor, C-terminal domain superfamily	Homologous Superfamily
A, D [auth B]	IPR021673	RIG-I-like receptor, C-terminal regulatory domain	Domain
A, D [auth B]	IPR031964	Caspase recruitment domain	Domain
A, D [auth B]	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, D [auth B]	IPR016024	Armadillo-type fold	Homologous Superfamily
A, D [auth B]	IPR006935	Helicase/UvrB, N-terminal	Domain
A, D [auth B]	IPR001650	Helicase, C-terminal domain-like	Domain
A, D [auth B]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, D [auth B]	IPR051363	RIG-I-like Receptor (RLR) Helicase	Family
A, D [auth B]	IPR041204	RIG-I-like receptor, C-terminal	Domain
A, D [auth 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.