5GS0

Crystal structure of the complex of TLR3 and bi-specific diabody

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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	PF13855	e5gs0A1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: PF13855	ECOD (1.6)
D [auth B]	PF13855	e5gs0B1	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats (From Topology)	T: Leucine-rich repeats	F: PF13855	ECOD (1.6)
B [auth C]	PF07686	e5gs0C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E	PF07686	e5gs0E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth D]	PF07686	e5gs0D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F	PF07686	e5gs0F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
G [auth X]	PF07686	e5gs0X1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth H]	PF07686	e5gs0H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth Y]	PF07686	e5gs0Y1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
J [auth L]	PF07686	e5gs0L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

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)
D [auth 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)
B [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A, D [auth B]	Toll-like receptor 3 (O15455)	TLR (Toll-like receptor)	Homo sapiens (human)	TLR3*01	R-LIKE-DOMAIN LRRNT, R-LIKE-DOMAIN LRR1, R-LIKE-DOMAIN LRR2, R-LIKE-DOMAIN LRR3, R-LIKE-DOMAIN LRR4, R-LIKE-DOMAIN LRR5, R-LIKE-DOMAIN LRR6, R-LIKE-DOMAIN LRR7, R-LIKE-DOMAIN LRR8, R-LIKE-DOMAIN LRR9, R-LIKE-DOMAIN LRR10, R-LIKE-DOMAIN LRR11, R-LIKE-DOMAIN LRR12, R-LIKE-DOMAIN LRR13, R-LIKE-DOMAIN LRR14, R-LIKE-DOMAIN LRR15, R-LIKE-DOMAIN LRR16, R-LIKE-DOMAIN LRR17, R-LIKE-DOMAIN LRR18, R-LIKE-DOMAIN LRR19, R-LIKE-DOMAIN LRR20, R-LIKE-DOMAIN LRR21, R-LIKE-DOMAIN LRR22, R-LIKE-DOMAIN LRRCT	RPI	TLR3	IMGT (202416-0)
B [auth C], E	Antibody Fab Fragment, anti-TLR3	V-LAMBDA	Homo sapiens (human)	IGLV3-2101, IGLV3-2102, IGLJ201, IGLJ302, IGLJ101, IGLJ301	V-DOMAIN V-LAMBDA	IG	FV-HEAVY_LAMBDA	IMGT (202416-0)
C [auth D], F	Antibody Fab Fragment, anti-TLR3	VH	Homo sapiens (human)	IGHV6-101, IGHV6-102, IGHJ401, IGHJ402, IGHJ4*03	V-DOMAIN VH	IG	FV-HEAVY_LAMBDA	IMGT (202416-0)
G [auth X], I [auth H]	Antibody Fab Fragment, anti-Lid	VH	Mus musculus (house mouse)	IGHV3-602, IGHV3-601, IGHJ3*01	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202416-0)
H [auth Y], J [auth L]	Antibody Fab Fragment, anti-Lid	V-KAPPA	Mus musculus (house mouse)	IGKV10-9601, IGKJ101	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth C], E	Light Chain	IGLV3	Lambda	toll-like receptor 3	SAbDab (2024-04-26)
C [auth D], F	Heavy Chain	IGHV6	-	toll-like receptor 3	SAbDab (2024-04-26)
G [auth X], I [auth H]	Heavy Chain	IGHV3	-	-	SAbDab (2024-04-26)
H [auth Y], J [auth L]	Light Chain	IGKV10	Kappa	-	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	PF13855	Leucine rich repeat (LRR_8)	Leucine rich repeat	-	Repeat
A, D [auth B]	PF13516	Leucine Rich repeat (LRR_6)	Leucine Rich repeat	-	Repeat
A, D [auth B]	PF00560	Leucine Rich Repeat (LRR_1)	Leucine Rich Repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth B]	Toll-like receptor 3	RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity pattern recognition receptor activity	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 cellular process cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic 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 response to interferon-beta response to organic substance response to cytokine cellular response to interferon-beta cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to organic substance 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 regulation of phosphate 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 organonitrogen compound metabolic process positive regulation of transferase 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 immune system process regulation of cytokine production involved in immune response immune effector process regulation of macrophage cytokine production 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 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 positive regulation of cytokine production involved in immune response macrophage cytokine production inflammatory response to wounding response to wounding 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 nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process 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 response to organic cyclic 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 cellular response to organic cyclic compound 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 I-kappaB phosphorylation regulation of non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction 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	membrane cellular anatomical entity 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 membrane cellular anatomical entity 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 extracellular region extracellular space endolysosome membrane endolysosome cell periphery plasma membrane extracellular matrix external encapsulating structure organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane early endosome
B [auth C], E	light chain (anti-TLR3)	-	-	-
C [auth D], F	heavy chain (anti-TLR3)	-	-	-
G [auth X], I [auth H]	heavy chain (anti-Lid)	-	-	-
H [auth Y], J [auth L]	light chain (anti-Lid)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR001611	Leucine-rich repeat	Repeat
A, D [auth B]	IPR017241	Toll-like receptor	Family
A, D [auth B]	IPR035897	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Homologous Superfamily
A, D [auth B]	IPR000483	Cysteine-rich flanking region, C-terminal	Domain
A, D [auth B]	IPR000157	Toll/interleukin-1 receptor homology (TIR) domain	Domain
A, D [auth B]	IPR003591	Leucine-rich repeat, typical subtype	Repeat
A, D [auth B]	IPR041015	Toll-like receptor 3 trans-membrane domain	Domain
A, D [auth B]	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D [auth B]	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 susceptibility to HIV infection ductal breast carcinoma in situ influenza juvenile dermatomyositis lung carcinoma malignant glioma breast cancer ovarian cancer Crohn disease schizophrenia transitional cell carcinoma encephalitis glioblastoma herpes simplex encephalitis

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 R01GM133198.