7BER | pdb_00007ber

SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt and refined using an identical protocol to the MicroED structure of the MyD88 TIR domain higher-order assembly)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
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)
A	d7bera_	Alpha and beta proteins (a/b)	Flavodoxin-like	Toll/Interleukin receptor TIR domain	automated matches	automated matches	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)
A	TIR	e7berA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Toll/Interleukin receptor TIR domain (From Topology)	T: Toll/Interleukin receptor TIR domain	F: TIR	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13676	TIR domain (TIR_2)	TIR domain	This is a family of Toll-like receptors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Myeloid differentiation primary response protein MyD88	protein binding binding signaling receptor binding Toll-like receptor binding catalytic activity, acting on a protein catalytic activity, acting on a nucleic acid histone chaperone activity ATP-dependent activity ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA protein carrier chaperone ATP-dependent histone chaperone activity catalytic activity protein binding binding signaling receptor binding Toll-like receptor binding catalytic activity, acting on a protein catalytic activity, acting on a nucleic acid histone chaperone activity ATP-dependent activity ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA protein carrier chaperone ATP-dependent histone chaperone activity catalytic activity molecular carrier activity Toll binding interleukin-1 receptor binding cytokine receptor binding growth factor receptor binding TIR domain binding protein domain specific binding tumor necrosis factor receptor superfamily binding death receptor binding molecular adaptor activity identical protein binding protein-macromolecule adaptor activity signaling adaptor activity	regulation of biological process regulation of cell motility regulation of cellular process regulation of leukocyte migration biological regulation neutrophil migration granulocyte migration leukocyte migration immune system process regulation of locomotion myeloid leukocyte migration regulation of cell migration cell migration cellular process regulation of biological process regulation of cell motility regulation of cellular process regulation of leukocyte migration biological regulation neutrophil migration granulocyte migration leukocyte migration immune system process regulation of locomotion myeloid leukocyte migration regulation of cell migration cell migration cellular process regulation of immune system process cell motility regulation of neutrophil migration locomotion adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus 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 pattern recognition receptor signaling pathway regulation of response to external stimulus toll-like receptor signaling pathway signaling positive regulation of biological process response to biotic stimulus 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 response to external biotic stimulus signal transduction positive regulation of immune system process innate immune response-activating signaling pathway MyD88-dependent toll-like receptor signaling pathway positive regulation of innate immune response defense response response to other organism regulation of innate immune response defense response to symbiont response to external stimulus regulation of response to stimulus 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 low-density lipoprotein particle stimulus cellular response to oxidised low-density lipoprotein particle stimulus response to endogenous stimulus response to chemical response to lipoprotein particle response to nitrogen compound cellular response to lipoprotein particle stimulus localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport 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 cell surface receptor signaling pathway interleukin-33-mediated signaling pathway response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to cytokine stimulus apoptotic process cell death programmed cell death developmental process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation endothelial cell development establishment of endothelial intestinal barrier epithelial cell development cell differentiation establishment of endothelial barrier anatomical structure development Toll signaling pathway multicellular organismal process chemokine (C-X-C motif) ligand 2 production regulation of chemokine production regulation of chemokine (C-X-C motif) ligand 2 production regulation of cytokine production cytokine production chemokine production regulation of multicellular organismal process defense response to bacterium response to bacterium interleukin-1 production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production positive regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production immune response-regulating cell surface receptor signaling pathway cell surface toll-like receptor signaling pathway immune response-activating cell surface receptor signaling pathway toll-like receptor 5 signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication positive regulation of signaling defense response to protozoan response to protozoan positive regulation of chemokine production positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function 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 regulation of molecular function regulation of DNA-binding transcription factor activity regulation of DNA-templated transcription positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation lymphocyte activation leukocyte proliferation leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation lymphocyte proliferation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation cell activation positive regulation of lymphocyte proliferation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of smooth muscle cell proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation muscle cell proliferation regulation of immune effector process positive regulation of myeloid leukocyte cytokine production involved in immune response positive regulation of immune effector process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response regulation of cytokine production involved in immune response regulation of macrophage cytokine production positive regulation of cytokine production involved in immune response positive regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response positive regulation of macrophage cytokine production macrophage cytokine production leukocyte activation involved in inflammatory response inflammatory response induced systemic resistance negative regulation of biological process post-transcriptional regulation of gene expression negative regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA stabilization mRNA catabolic process negative regulation of metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process negative regulation of RNA metabolic process catabolic process macromolecule catabolic process negative regulation of mRNA metabolic process 3'-UTR-mediated mRNA stabilization regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of catabolic process negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of catabolic process mRNA metabolic process regulation of mRNA stability RNA stabilization negative regulation of biosynthetic process regulation of RNA stability regulation of mRNA metabolic process toll-like receptor 8 signaling pathway cytoplasmic pattern recognition receptor signaling pathway intracellular receptor signaling pathway endolysosomal toll-like receptor signaling pathway defense response to virus response to virus positive regulation of type I interferon production type I interferon production regulation of type I interferon production positive regulation of DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process response to molecule of fungal origin response to fungus interferon-mediated signaling pathway cellular response to type I interferon type I interferon-mediated signaling pathway response to type I interferon response to acid chemical response to amino acid positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction toll-like receptor 4 signaling pathway skin development animal organ development interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production neutrophil-mediated killing of symbiont cell disruption of cell in another organism myeloid leukocyte mediated immunity biological process involved in symbiotic interaction neutrophil mediated immunity biological process involved in interaction with symbiont killing of cells of another organism neutrophil-mediated killing of bacterium neutrophil mediated cytotoxicity leukocyte mediated cytotoxicity killing by host of symbiont cells disruption of anatomical structure in another organism cell killing response to lipid cellular response to lipopolysaccharide lipopolysaccharide-mediated signaling pathway cellular response to biotic stimulus response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to lipid response to molecule of bacterial origin response to interleukin-1 myeloid leukocyte differentiation hemopoiesis macrophage differentiation mononuclear cell differentiation nervous system development multicellular organism development neurogenesis central nervous system development gliogenesis glial cell differentiation myeloid cell differentiation microglia differentiation system development leukocyte differentiation response to alcohol response to ethanol regulation of NLRP3 inflammasome complex assembly positive regulation of NLRP3 inflammasome complex assembly cellular component biogenesis cellular component assembly inflammasome-mediated signaling pathway canonical inflammasome complex assembly positive regulation of pattern recognition receptor signaling pathway positive regulation of inflammasome-mediated signaling pathway regulation of inflammasome-mediated signaling pathway regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly regulation of cellular component organization positive regulation of cellular component organization regulation of cytoplasmic pattern recognition receptor signaling pathway cellular component organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis regulation of inflammatory response response to mechanical stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus toll-like receptor TLR6:TLR2 signaling pathway positive regulation of interleukin-23 production interleukin-23 production regulation of interleukin-23 production interleukin-17 production regulation of interleukin-17 production positive regulation of interleukin-17 production cellular response to interleukin-1 interleukin-1-mediated signaling pathway regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response positive regulation of cytokine production involved in inflammatory response 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 response to peptidoglycan chemokine (C-X-C motif) ligand 1 production regulation of chemokine (C-X-C motif) ligand 1 production response to amine defense response to Gram-positive bacterium neutrophil activation cell activation involved in immune response myeloid leukocyte activation myeloid cell activation involved in immune response neutrophil activation involved in immune response leukocyte activation involved in immune response granulocyte activation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery extrinsic component of plasma membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane membrane plasma membrane extrinsic component of membrane extrinsic component of cytoplasmic side of plasma membrane side of membrane endosome membrane cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery extrinsic component of plasma membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane membrane plasma membrane extrinsic component of membrane extrinsic component of cytoplasmic side of plasma membrane side of membrane endosome membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle vesicle organelle membrane cell surface protein-containing complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000488	Death domain	Domain
A	IPR035897	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Homologous Superfamily
A	IPR000157	Toll/interleukin-1 receptor homology (TIR) domain	Domain
A	IPR011029	Death-like domain superfamily	Homologous Superfamily
A	IPR034249	MyD88, death domain	Domain
A	IPR017281	Myeloid differentiation primary response protein MyD88	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q99836	diffuse large B-cell lymphoma pyogenic bacterial infections due to MyD88 deficiency Waldenstrom macroglobulinemia follicular lymphoma pneumonia hypertensive disorder lymphoplasmacytic lymphoma Neoplasm Invasiveness macroglobulinemia extrahepatic cholestasis hypereosinophilic syndrome ischemia reperfusion injury lung cancer lymphoma arthritic joint disease diffuse large B-cell lymphoma pyogenic bacterial infections due to MyD88 deficiency Waldenstrom macroglobulinemia follicular lymphoma pneumonia hypertensive disorder lymphoplasmacytic lymphoma Neoplasm Invasiveness macroglobulinemia extrahepatic cholestasis hypereosinophilic syndrome ischemia reperfusion injury lung cancer lymphoma arthritic joint disease cancer congenital anemia macroglobulinemia, Waldenstrom, 1 multiple sclerosis ovarian cancer glioblastoma psoriasis subependymal giant cell astrocytoma juvenile dermatomyositis lung carcinoma astrocytic tumor cutaneous lupus erythematosus malignant glioma pancreatic intraductal papillary-mucinous neoplasm pneumonitis hematologic disease lymphatic system disease autoimmune disease colitis malignant mesothelioma pilocytic astrocytoma primitive neuroectodermal tumor

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.