2Z66 | pdb_00002z66

Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Hydrolase	e2z66A1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Hydrolase	ECOD (develop294)
B	Hydrolase	e2z66B1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Hydrolase	ECOD (develop294)
C	Hydrolase	e2z66C1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Hydrolase	ECOD (develop294)
D	Hydrolase	e2z66D1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Hydrolase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
B	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
C	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)
D	3.80.10.10	Alpha Beta	Alpha-Beta Horseshoe	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	Ribonuclease Inhibitor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Variable lymphocyte receptor B, Toll-like receptor 4	amyloid-beta binding binding peptide binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein binding signaling receptor binding lipid binding lipopolysaccharide binding carbohydrate derivative binding pattern recognition receptor activity lipopolysaccharide immune receptor activity identical protein binding amyloid-beta binding binding peptide binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein binding signaling receptor binding lipid binding lipopolysaccharide binding carbohydrate derivative binding pattern recognition receptor activity lipopolysaccharide immune receptor activity identical protein binding protein heterodimerization activity protein dimerization activity	regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process positive regulation of cellular process multicellular organismal process interleukin-1 production positive regulation of macromolecule biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of interleukin-1 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of tumor necrosis factor production negative regulation of biological process negative regulation of tumor necrosis factor production negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of metabolic process tumor necrosis factor superfamily cytokine production negative regulation of cytokine production tumor necrosis factor production negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production negative regulation of multicellular organismal process connective tissue development developmental growth endochondral bone morphogenesis organ growth multicellular organism development skeletal system development growth plate cartilage development anatomical structure development endochondral bone growth animal organ morphogenesis bone development system development developmental process growth plate cartilage morphogenesis growth animal organ development tissue development anatomical structure morphogenesis tissue morphogenesis bone growth cartilage morphogenesis skeletal system morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis cartilage development cellular response to stimulus cellular response to low-density lipoprotein particle stimulus cellular response to oxidised low-density lipoprotein particle stimulus response to stimulus response to endogenous stimulus response to chemical response to lipoprotein particle cellular response to lipoprotein particle stimulus regulation of localization establishment of protein localization regulation of protein localization transport matrix metallopeptidase secretion positive regulation of matrix metallopeptidase secretion positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport localization secretion by cell regulation of secretion by cell positive regulation of secretion intracellular protein localization regulation of matrix metallopeptidase secretion secretion regulation of transport establishment of protein localization to extracellular region regulation of establishment of protein localization export from cell regulation of protein transport protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport macromolecule localization positive regulation of protein localization signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion defense response to bacterium biological process involved in interspecies interaction between organisms response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus positive regulation of cell communication positive regulation of response to biotic stimulus positive regulation of signal transduction pattern recognition receptor signaling pathway immune response-activating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway immune response regulation of innate immune response positive regulation of intracellular signal transduction positive regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway 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 activation of immune response regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus intracellular receptor signaling pathway regulation of cytoplasmic pattern recognition receptor signaling pathway positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress innate immune response nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway nucleotide-binding oligomerization domain containing 2 signaling pathway positive regulation of innate immune response regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway defense response to symbiont positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway immune system process positive regulation of signaling positive regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production regulation of chemokine production chemokine production positive regulation of chemokine production JNK cascade cellular response to lipoteichoic acid response to oxygen-containing compound response to lipoteichoic acid cellular response to molecule of bacterial origin cellular response to oxygen-containing compound cellular response to biotic stimulus cellular response to chemical stimulus response to molecule of bacterial origin interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation regulation of type II interferon production type II interferon production negative regulation of type II interferon production defense response to Gram-negative bacterium 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 immune effector process 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 system process epithelial structure maintenance homeostatic process digestive system process intestinal epithelial structure maintenance tissue homeostasis maintenance of gastrointestinal epithelium digestion multicellular organismal-level homeostasis anatomical structure homeostasis interleukin-17 production negative regulation of interleukin-17 production regulation of interleukin-17 production B cell proliferation involved in immune response B cell activation cell activation B cell proliferation B cell activation involved in immune response lymphocyte activation cell activation involved in immune response leukocyte proliferation leukocyte activation mononuclear cell proliferation leukocyte activation involved in immune response lymphocyte proliferation lymphocyte activation involved in immune response 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 positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction regulation of macrophage activation positive regulation of macrophage activation regulation of leukocyte activation regulation of cell activation myeloid leukocyte activation macrophage activation positive regulation of cell activation positive regulation of leukocyte activation positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade regulation of programmed cell death extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of programmed cell death cell surface receptor signaling pathway regulation of apoptotic process positive regulation of extrinsic apoptotic signaling pathway cell death positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production toll-like receptor signaling pathway TRIF-dependent toll-like receptor signaling pathway MyD88-independent toll-like receptor signaling pathway regulation of interferon-beta production interferon-beta production positive regulation of interferon-beta production myeloid leukocyte differentiation cellular developmental process hemopoiesis macrophage differentiation cell development mononuclear cell differentiation nervous system development neurogenesis central nervous system development gliogenesis glial cell differentiation myeloid cell differentiation cell differentiation microglia differentiation leukocyte differentiation 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 inflammasome-mediated signaling pathway regulation of inflammasome-mediated signaling pathway NLRP3 inflammasome complex assembly inflammatory response regulation of cellular component organization positive regulation of cellular component organization 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 response to type II interferon response to cytokine cellular response to type II interferon response to peptide cellular response to cytokine stimulus 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 reactive oxygen species biosynthetic process positive regulation of reactive oxygen species biosynthetic process reactive oxygen species metabolic process regulation of reactive oxygen species biosynthetic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process regulation of MHC class II biosynthetic process MHC class II biosynthetic process positive regulation of MHC class II biosynthetic process 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 body fluid levels positive regulation of platelet activation coagulation regulation of biological quality response to wounding wound healing hemostasis blood coagulation regulation of platelet activation platelet activation positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production negative regulation of cold-induced thermogenesis adaptive thermogenesis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis cellular response to nitrogen compound response to nitrogen compound cellular response to amyloid-beta response to amyloid-beta response to lipid response to lipopolysaccharide positive regulation of type II interferon production regulation of cellular response to stress stress-activated MAPK cascade cellular response to stress positive regulation of stress-activated protein kinase signaling cascade positive regulation of stress-activated MAPK cascade regulation of stress-activated protein kinase signaling cascade regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade MyD88-dependent toll-like receptor signaling pathway regulation of inflammatory response positive regulation of inflammatory response interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production import into cell phagocytosis endocytosis vesicle-mediated transport interleukin-23 production regulation of interleukin-23 production negative regulation of interleukin-23 production nucleotide-binding oligomerization domain containing 1 signaling pathway regulation of leukocyte differentiation regulation of developmental process regulation of cell differentiation regulation of cell development regulation of osteoclast differentiation osteoclast differentiation negative regulation of cell differentiation negative regulation of hemopoiesis regulation of multicellular organismal development negative regulation of leukocyte differentiation regulation of myeloid cell differentiation negative regulation of developmental process regulation of myeloid leukocyte differentiation negative regulation of myeloid cell differentiation negative regulation of osteoclast differentiation negative regulation of myeloid leukocyte differentiation negative regulation of cell development negative regulation of immune system process regulation of hemopoiesis astrocyte differentiation glial cell development astrocyte development regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production interleukin-1 beta production chemokine (C-X-C motif) ligand 2 production regulation of chemokine (C-X-C motif) ligand 2 production positive regulation of chemokine (C-X-C motif) ligand 2 production positive regulation of JNK cascade regulation of JNK cascade wound healing involved in inflammatory response inflammatory response to wounding nitric oxide production involved in inflammatory response positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway positive regulation of B cell proliferation positive regulation of lymphocyte activation regulation of B cell proliferation regulation of B cell activation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation positive regulation of B cell activation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation 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 detection of external biotic stimulus detection of lipopolysaccharide detection of molecule of bacterial origin detection of biotic stimulus detection of stimulus detection of chemical stimulus immune response-regulating cell surface receptor signaling pathway cell surface toll-like receptor signaling pathway immune response-activating cell surface receptor signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway toll-like receptor 4 signaling pathway cellular response to endogenous stimulus cellular response to growth factor stimulus cellular response to platelet-derived growth factor stimulus response to growth factor response to platelet-derived growth factor positive regulation of interleukin-6 production cellular response to lipopolysaccharide lipopolysaccharide-mediated signaling pathway cellular response to lipid dendritic cell cytokine production regulation of dendritic cell cytokine production leukocyte mediated immunity regulation of leukocyte mediated immunity regulation of response to macrophage colony-stimulating factor response to macrophage colony-stimulating factor positive regulation of response to cytokine stimulus cellular response to macrophage colony-stimulating factor stimulus regulation of response to cytokine stimulus regulation of cellular response to macrophage colony-stimulating factor stimulus positive regulation of response to macrophage colony-stimulating factor positive regulation of cellular response to macrophage colony-stimulating factor stimulus detection of other organism response to fungus detection of fungus adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains T-helper 1 type immune response adaptive immune response	protein-containing complex receptor complex endosome membrane membrane-bounded organelle intracellular anatomical structure membrane endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle protein-containing complex receptor complex endosome membrane membrane-bounded organelle intracellular anatomical structure membrane endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane phagocytic cup cell periphery plasma membrane cell surface external side of plasma membrane side of membrane ruffle cell projection cell leading edge plasma membrane bounded cell projection perinuclear region of cytoplasm lipopolysaccharide receptor complex membrane protein complex early endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR035897	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Homologous Superfamily
A, B, C, D	IPR000483	Cysteine-rich flanking region, C-terminal	Domain
A, B, C, D	IPR000157	Toll/interleukin-1 receptor homology (TIR) domain	Domain
A, B, C, D	IPR025875	Leucine rich repeat 4	Repeat
A, B, C, D	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B, C, D	IPR001611	Leucine-rich repeat	Repeat
A, B, C, D	IPR017241	Toll-like receptor	Family
A, B, C, D	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A, B, C, D	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B, C, D	IPR000372	Leucine-rich repeat N-terminal domain	Domain
A, B, C, D	IPR024592	Variable_lymphocyte_rcpt_C	Unknown
A, B, C, D	IPR001611	Leucine-rich repeat	Repeat
A, B, C, D	IPR050541	Leucine-rich repeat and transmembrane domain-containing protein	Family
A, B, C, D	IPR003591	Leucine-rich repeat, typical subtype	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O00206	hypertensive disorder pneumonia age-related macular degeneration contact dermatitis melanoma coronary artery disease esophageal adenocarcinoma Crohn disease atherosclerosis diabetic polyneuropathy Behcet disease Liver Cirrhosis, Experimental acute coronary syndrome hepatocellular carcinoma kidney failure hypertensive disorder pneumonia age-related macular degeneration contact dermatitis melanoma coronary artery disease esophageal adenocarcinoma Crohn disease atherosclerosis diabetic polyneuropathy Behcet disease Liver Cirrhosis, Experimental acute coronary syndrome hepatocellular carcinoma kidney failure perinatal necrotizing enterocolitis colorectal cancer diabetic autonomic neuropathy ovarian cancer diabetic neuropathy prostate cancer extrahepatic cholestasis carcinoma sarcomatoid carcinoma hearing loss disorder large cell medulloblastoma peripheral nervous system disease exocrine pancreatic carcinoma lung adenocarcinoma breast fibroadenoma lung carcinoma retinal degeneration macular degeneration schizophrenia Gaucher disease medulloblastoma IgA glomerulonephritis Crohn's colitis cutaneous melanoma ulcerative colitis arthritic joint disease non-alcoholic fatty liver disease osteosarcoma atypical teratoid rhabdoid tumor learning disability bipolar disorder peripheral neuropathy pneumonitis liver disease brain injury psoriasis lung benign neoplasm cancer cerebrovascular disorder rheumatoid arthritis gastric cancer acute kidney failure malignant glioma glioblastoma adrenal cortex carcinoma skin disease hypereosinophilic syndrome alcohol abuse ileocolitis cystic fibrosis undifferentiated carcinoma inflammatory bowel disease asthma non-small cell lung carcinoma ischemia reperfusion injury autoimmune disease periodontitis endogenous depression pilocytic astrocytoma lung cancer fatty liver disease gastric carcinoma malignant mesothelioma colorectal carcinoma age related macular degeneration 10 malignant pancreatic neoplasm allergic disease necrotizing enterocolitis type 2 diabetes mellitus inborn carbohydrate metabolic disorder arteriosclerosis disorder neurodegenerative disease influenza astrocytic tumor obesity disorder kidney disease ovarian neoplasm

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.