9TOY | pdb_00009toy

Investigating the binding mechanism of Interferon Regulatory Factor 4 to DNA in the context of Multiple Myeloma

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Winged helix DNA-binding domain	8077685	3000034	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	Winged helix DNA-binding domain	8077685	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8077685	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8077685	3000034	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E [auth D], F	PF00605	Interferon regulatory factor transcription factor (IRF)	Interferon regulatory factor transcription factor	This family of transcription factors are important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. Three of the five conserved tryptophan residues bind to DNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, E [auth D], F	Interferon regulatory factor 4	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription coactivator activity transcription regulator activity transcription coregulator activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription coactivator activity transcription regulator activity transcription coregulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus toll-like receptor signaling pathway negative regulation of biological process regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction cellular response to stimulus positive regulation of response to biotic stimulus regulation of cellular process pattern recognition receptor signaling pathway response to stimulus toll-like receptor signaling pathway negative regulation of biological process regulation of signal transduction response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway regulation of biological process immune response response to other organism regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response regulation of toll-like receptor signaling pathway activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus signaling negative regulation of signaling positive regulation of biological process negative regulation of cell communication positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response negative regulation of cellular process response to external biotic stimulus regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus biological regulation defense response to symbiont negative regulation of signal transduction negative regulation of toll-like receptor signaling pathway negative regulation of immune system process immune system process regulation of cell communication cellular process developmental process multicellular organismal process myeloid leukocyte differentiation cellular developmental process myeloid dendritic cell activation hemopoiesis cell activation cell development mononuclear cell differentiation myeloid leukocyte activation leukocyte activation myeloid cell differentiation cell differentiation anatomical structure development myeloid dendritic cell differentiation dendritic cell differentiation leukocyte differentiation interleukin-13 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of interleukin-13 production positive regulation of gene expression positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process regulation of interleukin-13 production T cell activation lymphocyte activation defense response to protozoan response to protozoan homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis regulation of interleukin-2 production interleukin-2 production positive regulation of interleukin-2 production interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process 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 transcription by RNA polymerase II regulation of transcription by RNA polymerase II regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production regulation of leukocyte differentiation regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation regulation of cell differentiation lymphocyte differentiation regulation of cell development multicellular organism development regulation of T-helper cell differentiation alpha-beta T cell activation T cell differentiation T-helper cell differentiation regulation of developmental process regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation regulation of T cell differentiation alpha-beta T cell differentiation CD4-positive, alpha-beta T cell activation regulation of lymphocyte differentiation regulation of multicellular organismal development regulation of T cell activation regulation of CD4-positive, alpha-beta T cell activation regulation of hemopoiesis regulation of lymphocyte activation positive regulation of transcription by RNA polymerase II cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis CD4-positive or CD8-positive, alpha-beta T cell lineage commitment adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains cell activation involved in immune response T cell activation involved in immune response alpha-beta T cell activation involved in immune response leukocyte activation involved in immune response CD4-positive, alpha-beta T cell lineage commitment lymphocyte activation involved in immune response alpha-beta T cell lineage commitment T-helper cell lineage commitment T cell differentiation involved in immune response T cell lineage commitment adaptive immune response immune effector process T-helper 17 cell lineage commitment positive T cell selection T cell selection T-helper 17 cell differentiation cell fate commitment T-helper 17 type immune response	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle organelle membraneless organelle cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle organelle membraneless organelle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C, G	DNA (5'-D(PTPCPAPAPCPTPGPAPAPAPCPTPGPAPGPAPAPAPGPC)-3')	-	-	-
D [auth E], H	DNA (5'-D(PAPGPCPTPTPTPCPTPCPAPGPTPTPTPCPAPGPTPTPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E [auth D], F	IPR001346	Interferon regulatory factor, DNA-binding domain	Domain
A, B, E [auth D], F	IPR019817	Interferon regulatory factor, conserved site	Conserved Site
A, B, E [auth D], F	IPR019471	Interferon regulatory factor-3	Domain
A, B, E [auth D], F	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A, B, E [auth D], F	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, E [auth D], F	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, E [auth D], F	IPR017855	SMAD-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, E [auth D], F	Pharos: Q15306	plasma cell myeloma B-cell chronic lymphocytic leukemia adult T-cell leukemia/lymphoma progressive supranuclear palsy melanoma primary cutaneous T-cell non-Hodgkin lymphoma periodontitis squamous cell carcinoma acute T cell leukemia Waldenstrom macroglobulinemia Crohn disease Hashimoto thyroiditis interstitial cystitis Lymphoma, T-Cell, Cutaneous myeloid neoplasm plasma cell myeloma B-cell chronic lymphocytic leukemia adult T-cell leukemia/lymphoma progressive supranuclear palsy melanoma primary cutaneous T-cell non-Hodgkin lymphoma periodontitis squamous cell carcinoma acute T cell leukemia Waldenstrom macroglobulinemia Crohn disease Hashimoto thyroiditis interstitial cystitis Lymphoma, T-Cell, Cutaneous myeloid neoplasm peripheral nervous system disease plasma cell neoplasm rheumatoid arthritis ulcerative colitis cancer diffuse large B-cell lymphoma hematologic disease lung cancer osteosarcoma peripheral neuropathy skin basal cell carcinoma vitiligo androgenetic alopecia celiac disease granulomatous slack skin disease inflammatory bowel disease lymphatic system disease membranous glomerulonephritis

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.