2QFD | pdb_00002qfd

Crystal structure of the regulatory domain of human RIG-I with bound Hg

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)
J	d2qfdj_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d2qfdi_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2qfdh_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d2qfdg_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2qfdf_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2qfde_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2qfdd_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2qfdc_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2qfdb_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2qfda_	All beta proteins	Mss4-like	RIG-I C-terminal-like	RIG-I C-terminal domain-like	RIG-I C-terminal domain	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)
J	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Mss4-like	8103677	3001994	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mss4-like	8103677	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)
J	RIG-I_C-RD	e2qfdJ1	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)
I	RIG-I_C-RD	e2qfdI1	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)
H	RIG-I_C-RD	e2qfdH1	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)
G	RIG-I_C-RD	e2qfdG1	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)
F	RIG-I_C-RD	e2qfdF1	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)
E	RIG-I_C-RD	e2qfdE1	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	RIG-I_C-RD	e2qfdD1	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)
C	RIG-I_C-RD	e2qfdC1	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)
B	RIG-I_C-RD	e2qfdB1	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	RIG-I_C-RD	e2qfdA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
I	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
H	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
G	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
F	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
E	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
D	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
C	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
B	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
A	2.170.150.30	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF11648	C-terminal domain of RIG-I (RIG-I_C-RD)	C-terminal domain of RIG-I	This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependen ...	This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	Probable ATP-dependent RNA helicase DDX58	RNA binding double-stranded RNA binding binding nucleic acid 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 RNA binding double-stranded RNA binding binding nucleic acid 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 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 catalytic activity ATP-dependent activity ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding identical protein binding single-stranded RNA binding molecular transducer activity pattern recognition receptor activity signaling receptor activity guanyl nucleotide binding GTP binding guanyl ribonucleotide binding DNA binding double-stranded DNA 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 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 regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process RIG-I signaling pathway regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion response to cytokine positive regulation of response to cytokine stimulus response to peptide regulation of response to cytokine stimulus response to chemical multicellular organismal process positive regulation of interleukin-8 production cytokine production regulation of cytokine production regulation of multicellular organismal process interleukin-8 production positive regulation of multicellular organismal process positive regulation of cytokine production regulation of interleukin-8 production regulation of immune effector process positive regulation of leukocyte mediated immunity regulation of myeloid leukocyte mediated immunity myeloid leukocyte mediated immunity dendritic cell cytokine production leukocyte mediated immunity regulation of cytokine production involved in immune response immune effector process regulation of leukocyte mediated immunity myeloid dendritic cell cytokine production positive regulation of myeloid leukocyte mediated immunity positive regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response positive regulation of dendritic cell cytokine production regulation of myeloid dendritic cell cytokine production positive regulation of myeloid leukocyte cytokine production involved in immune response regulation of dendritic cell cytokine production positive regulation of immune effector process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response positive regulation of myeloid dendritic cell cytokine production positive regulation of cytokine production involved in immune response regulation of defense response to virus defense response to virus positive regulation of defense response to virus by host regulation of defense response to virus by host response to virus positive regulation of DNA-templated transcription 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription interferon-alpha production regulation of interferon-alpha production positive regulation of type I interferon production type I interferon production positive regulation of interferon-alpha production regulation of type I interferon production interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production response to dsRNA response to nitrogen compound response to exogenous dsRNA cellular response to nitrogen compound cellular response to dsRNA cellular response to exogenous dsRNA cellular response to chemical stimulus regulation of interferon-beta production interferon-beta production positive regulation of interferon-beta production antiviral innate immune response granulocyte macrophage colony-stimulating factor production positive regulation of protein metabolic process positive regulation of granulocyte macrophage colony-stimulating factor production protein metabolic process regulation of granulocyte macrophage colony-stimulating factor production regulation of protein metabolic process detection of virus regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production regulation of type III interferon production type III interferon production	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol ruffle cell leading edge plasma membrane membrane intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane cell-cell junction apical junction complex bicellular tight junction tight junction anchoring junction cell junction protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	Pharos: O95786	psoriasis Singleton-Merten syndrome 2 influenza hepatitis C virus infection pilocytic astrocytoma pustulosis palmaris et plantaris tuberculosis atopic eczema dermatomyositis glioblastoma juvenile dermatomyositis malignant glioma ovarian cancer singleton-Merten dysplasia Sjogren syndrome psoriasis Singleton-Merten syndrome 2 influenza hepatitis C virus infection pilocytic astrocytoma pustulosis palmaris et plantaris tuberculosis atopic eczema dermatomyositis glioblastoma juvenile dermatomyositis malignant glioma ovarian cancer singleton-Merten dysplasia Sjogren syndrome cutaneous lupus erythematosus Disease Exacerbation intellectual disability lung cancer microphthalmia with limb anomalies pancreatic intraductal papillary-mucinous neoplasm Singleton-Merten syndrome 1 systemic lupus erythematosus cystic fibrosis hepatocellular carcinoma interstitial cystitis malignant ependymoma osteosarcoma

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.