9LSJ | pdb_00009lsj

Cryo-EM structure of the G15C-R66C and T83C-T83C diabody complex (CitS-diabody #7-TLR3)

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	NTP_transf_3	e9lsjE01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: NTP_transf_3	ECOD (v294.1)
D	NTP_transf_3	e9lsjD01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: NTP_transf_3	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	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
E	Diabody (TLR3 VH-CitS VL)	-	-	-
D	Diabody (CitS VH-TLR3 VL)	-	-	-
C	Toll-like receptor 3	RNA binding double-stranded RNA binding binding nucleic acid binding identical protein binding protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity pattern recognition receptor activity ubiquitin-like protein ligase binding enzyme binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response regulation of biosynthetic process regulation of cellular 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 cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process type III interferon production positive regulation of type III interferon production regulation of type III interferon production positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus cellular response to stimulus cell surface receptor signaling pathway signaling extrinsic apoptotic signaling pathway cell communication apoptotic signaling pathway signal transduction myeloid leukocyte differentiation regulation of leukocyte differentiation cellular developmental process regulation of developmental process negative regulation of biological process cell development regulation of cell differentiation regulation of cell development regulation of osteoclast differentiation cell differentiation osteoclast differentiation negative regulation of cellular process regulation of immune system process negative regulation of cell differentiation negative regulation of hemopoiesis regulation of multicellular organismal development negative regulation of leukocyte differentiation hemopoiesis 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 myeloid cell differentiation negative regulation of immune system process regulation of hemopoiesis negative regulation of multicellular organismal process leukocyte differentiation cellular response to interferon-beta response to peptide response to interferon-beta response to chemical response to cytokine cellular response to cytokine stimulus defense response to bacterium response to bacterium necroptotic process programmed necrotic cell death necroptotic signaling pathway response to osmotic stress hyperosmotic response response to abiotic stimulus positive regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production 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 positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process phosphate-containing compound metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation activation of NF-kappaB-inducing kinase activity protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation non-canonical NF-kappaB signal transduction regulation of protein metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of molecular function positive regulation of protein modification process protein metabolic process positive regulation of protein kinase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of phosphorylation regulation of chemokine production chemokine production positive regulation of chemokine production 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 positive regulation of immune system process 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 inflammatory response to wounding response to wounding cellular response to chemical stimulus cellular response to xenobiotic stimulus response to xenobiotic stimulus positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway immune response-activating signaling pathway positive regulation of immune response innate immune response-activating signaling pathway regulation of innate immune response activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of response to biotic stimulus intracellular receptor signaling pathway endolysosomal toll-like receptor signaling pathway immune response-regulating signaling pathway positive regulation of innate immune response toll-like receptor 3 signaling pathway defense response to virus response to virus positive regulation of DNA-templated transcription RNA 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 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 cell activation myeloid leukocyte activation leukocyte activation macrophage activation leukocyte activation involved in inflammatory response microglial cell activation glial cell activation neuroinflammatory 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 response to dsRNA response to nitrogen compound positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production response to exogenous dsRNA cellular response to nitrogen compound cellular response to dsRNA cellular response to exogenous dsRNA regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production regulation of interferon-beta production interferon-beta production positive regulation of interferon-beta production dendritic cell cytokine production regulation of dendritic cell cytokine production leukocyte mediated immunity regulation of leukocyte mediated immunity response to type II interferon cellular response to type II interferon response to mechanical stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus angiogenesis regulation of vasculature development positive regulation of developmental process tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis 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 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 toll-like receptor signaling pathway regulation of type II interferon production type II interferon production positive regulation of type II interferon production cellular response to virus	cellular anatomical structure membrane intracellular anatomical structure cytoplasm vacuolar membrane membrane-bounded organelle lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cellular anatomical structure membrane intracellular anatomical structure cytoplasm vacuolar membrane membrane-bounded organelle lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane organelle membrane lysosome Golgi membrane Golgi apparatus endomembrane system endosome membrane endosome intracellular vesicle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle endolysosome membrane endolysosome cell periphery plasma membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane early endosome
A, B	Citrate/sodium symporter	active transmembrane transporter activity transporter activity symporter activity transmembrane transporter activity secondary active transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process citrate metabolic process localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport tricarboxylic acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process cellular process organic acid metabolic process citrate metabolic process localization transport monoatomic ion transport monoatomic cation transport establishment of localization sodium ion transport metal ion transport	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR001611	Leucine-rich repeat	Repeat
C	IPR035897	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Homologous Superfamily
C	IPR000483	Cysteine-rich flanking region, C-terminal	Domain
C	IPR000157	Toll/interleukin-1 receptor homology (TIR) domain	Domain
C	IPR003591	Leucine-rich repeat, typical subtype	Repeat
C	IPR041015	Toll-like receptor 3 trans-membrane domain	Domain
C	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B	IPR018025	2-hydroxycarboxylate transporter, proteobacteria/firmicutes	Family
A, B	IPR004679	2-hydroxycarboxylate transporter	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: O15455	herpes simplex encephalitis, susceptibility to, 2 HIV infectious disease hypothyroidism interstitial cystitis lung adenocarcinoma malignant colon neoplasm adenoma malignant mesothelioma breast carcinoma pilocytic astrocytoma cutaneous lupus erythematosus subependymal giant cell astrocytoma endometriosis Hashimoto thyroiditis herpes simplex encephalitis, susceptibility to, 1 herpes simplex encephalitis, susceptibility to, 2 HIV infectious disease hypothyroidism interstitial cystitis lung adenocarcinoma malignant colon neoplasm adenoma malignant mesothelioma breast carcinoma pilocytic astrocytoma cutaneous lupus erythematosus subependymal giant cell astrocytoma endometriosis Hashimoto thyroiditis herpes simplex encephalitis, susceptibility to, 1 HIV Coinfection idiopathic pulmonary fibrosis invasive ductal breast carcinoma lung cancer malignant ependymoma autoimmune disease non-small cell lung carcinoma cancer pituitary cancer ductal breast carcinoma in situ susceptibility to HIV infection influenza juvenile dermatomyositis lung carcinoma malignant glioma breast cancer ovarian cancer Crohn disease schizophrenia encephalitis transitional cell carcinoma glioblastoma herpes simplex encephalitis

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

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.

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