9QWK | pdb_00009qwk

Crystal structure of S2c-a5b6 TCR in complex with CD1c

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)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8003766	3000071	SCOP2B (2022-06-29)
H [auth J]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8003766	3000071	SCOP2B (2022-06-29)
L [auth O]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8003766	3000071	SCOP2B (2022-06-29)
P [auth T]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8003766	3000071	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	Beta-2-microglobulin,T-cell surface glycoprotein CD1c	binding lipid binding glycolipid binding carbohydrate derivative binding amide binding lipopeptide binding antigen binding exogenous lipid antigen binding lipid antigen binding endogenous lipid antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding binding lipid binding glycolipid binding carbohydrate derivative binding amide binding lipopeptide binding antigen binding exogenous lipid antigen binding lipid antigen binding endogenous lipid antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding identical protein binding protein binding protein homodimerization activity protein dimerization activity structural molecule activity	response to stimulus immune response immune system process adaptive immune response antigen processing and presentation antigen processing and presentation of lipid antigen via MHC class Ib antigen processing and presentation via MHC class Ib antigen processing and presentation of endogenous antigen antigen processing and presentation, endogenous lipid antigen via MHC class Ib antigen processing and presentation of exogenous antigen antigen processing and presentation, exogenous lipid antigen via MHC class Ib multicellular organismal process cell activation lymphocyte activation response to stimulus immune response immune system process adaptive immune response antigen processing and presentation antigen processing and presentation of lipid antigen via MHC class Ib antigen processing and presentation via MHC class Ib antigen processing and presentation of endogenous antigen antigen processing and presentation, endogenous lipid antigen via MHC class Ib antigen processing and presentation of exogenous antigen antigen processing and presentation, exogenous lipid antigen via MHC class Ib multicellular organismal process cell activation lymphocyte activation cell activation involved in immune response leukocyte activation immune effector process T cell activation involved in immune response T cell activation leukocyte activation involved in immune response cellular process lymphocyte activation involved in immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of immune response positive regulation of leukocyte mediated cytotoxicity leukocyte mediated immunity regulation of immune system process positive regulation of immune effector process positive regulation of adaptive immune response positive regulation of immune system process positive regulation of cellular process regulation of T cell mediated immunity T cell mediated cytotoxicity regulation of biological process positive regulation of T cell mediated cytotoxicity regulation of adaptive immune response biological regulation regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity regulation of leukocyte mediated immunity regulation of T cell mediated cytotoxicity regulation of lymphocyte mediated immunity regulation of response to stimulus positive regulation of T cell mediated immunity regulation of immune response regulation of cell killing positive regulation of cell killing cell killing intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process protein metabolic process macromolecule metabolic process T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process cytokine production positive regulation of macromolecule metabolic process positive regulation of T cell cytokine production regulation of cytokine production involved in immune response regulation of gene expression positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process regulation of T cell cytokine production positive regulation of biosynthetic process regulation of cytokine production regulation of multicellular organismal process cytokine production involved in immune response production of molecular mediator of immune response regulation of biosynthetic process regulation of macromolecule metabolic process positive regulation of gene expression positive regulation of cytokine production involved in immune response cellular response to stimulus cellular response to iron ion cellular response to metal ion cellular response to chemical stimulus response to metal ion response to iron ion response to chemical cellular response to iron(III) ion response to iron(III) ion multicellular organismal-level iron ion homeostasis multicellular organismal-level homeostasis multicellular organismal-level chemical homeostasis regulation of neuron projection development regulation of cellular component organization cellular developmental process cell projection organization negative regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization nervous system development negative regulation of neuron projection development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization regulation of developmental process regulation of cell differentiation regulation of cell development myeloid cell homeostasis erythrocyte homeostasis regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation erythrocyte differentiation regulation of erythrocyte differentiation myeloid cell differentiation regulation of hemopoiesis homeostasis of number of cells antigen processing and presentation of peptide antigen via MHC class Ib antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent antigen processing and presentation of exogenous peptide antigen via MHC class Ib antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen mononuclear cell differentiation lymphocyte differentiation T cell differentiation in thymus T cell differentiation leukocyte differentiation regulation of localization import into cell positive regulation of cellular component organization transport vesicle-mediated transport localization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of transport endocytosis receptor-mediated endocytosis peptide antigen assembly with MHC class I protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class I protein complex assembly cellular component biogenesis cellular component assembly protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class I MHC protein complex assembly regulation of neurogenesis regulation of nervous system development negative regulation of neurogenesis negative regulation of nervous system development negative regulation of cell differentiation negative regulation of developmental process negative regulation of cell development negative regulation of multicellular organismal process negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation establishment of protein localization nitrogen compound transport iron ion transport metal ion transport protein transport macromolecule localization transferrin transport transition metal ion transport monoatomic ion transport intracellular protein localization monoatomic cation transport system process sensory perception of chemical stimulus sensory perception nervous system process sensory perception of smell supramolecular fiber organization amyloid fibril formation protein homotetramerization protein complex oligomerization protein tetramerization protein homooligomerization antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II negative regulation of receptor binding regulation of protein binding regulation of molecular function regulation of receptor binding negative regulation of protein binding regulation of binding negative regulation of binding negative regulation of molecular function peptide antigen assembly with MHC class II protein complex MHC class II protein complex assembly cellular response to nicotine response to nicotine regulation of cellular senescence cellular senescence positive regulation of cellular senescence cellular response to stress response to stress antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of endogenous peptide antigen via MHC class I behavior learning or memory cognition regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion positive regulation of leukocyte activation regulation of cell-cell adhesion positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation regulation of leukocyte cell-cell adhesion regulation of lymphocyte activation negative regulation of forebrain neuron differentiation forebrain development regulation of forebrain neuron differentiation central nervous system neuron differentiation head development forebrain generation of neurons animal organ development brain development central nervous system development forebrain neuron differentiation negative regulation of neuron differentiation regulation of neuron differentiation regulation of monoatomic ion transport regulation of iron ion transport regulation of metal ion transport biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to molecule of bacterial origin response to biotic stimulus	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle lytic vacuole vacuole cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle lytic vacuole vacuole cytoplasm lysosome Golgi apparatus endomembrane system endosome membrane endosome intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle organelle membrane extracellular region extracellular space endoplasmic reticulum extracellular exosome extracellular vesicle extracellular organelle extracellular membrane-bounded organelle protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex HFE-transferrin receptor complex receptor complex cytosol MHC class I protein complex MHC protein complex late endosome membrane late endosome phagocytic vesicle phagocytic vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole membrane lysosomal membrane membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen Golgi membrane MHC class I peptide loading complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane vesicle lumen cytoplasmic vesicle lumen secretory granule lumen specific granule lumen secretory granule secretory vesicle specific granule anchoring junction cell junction focal adhesion cell-substrate junction MHC class II protein complex early endosome endosome lumen early endosome lumen recycling endosome recycling endosome membrane tertiary granule lumen tertiary granule early endosome membrane transport vesicle transport vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane coated vesicle
C [auth D], G [auth H], K [auth M], O [auth R]	TCR alpha	-	-	-
D [auth E], E [auth F], I [auth K], M [auth P]	TCR beta	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR050208	Antigen-presenting and immune regulatory MHC class I-related	Family
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR003597	Immunoglobulin C1-set	Domain
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR011161	MHC class I-like antigen recognition-like	Domain
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR007110	Immunoglobulin-like domain	Domain
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR007110	Immunoglobulin-like domain	Domain
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR003597	Immunoglobulin C1-set	Domain
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	IPR015707	Beta-2-Microglobulin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, F [auth G], H [auth J], J [auth L], A, B, F [auth G], H [auth J], J [auth L], L [auth O], N [auth Q], P [auth T]	Pharos: P61769	acute myeloid leukemia cutaneous lupus erythematosus Langerhans cell histiocytosis nasopharyngeal carcinoma skin disease B-cell chronic lymphocytic leukemia Erdheim-Chester disease lung cancer non-small cell lung carcinoma tuberculosis cancer juvenile xanthogranuloma lung carcinoma osteosarcoma familial visceral amyloidosis acute myeloid leukemia cutaneous lupus erythematosus Langerhans cell histiocytosis nasopharyngeal carcinoma skin disease B-cell chronic lymphocytic leukemia Erdheim-Chester disease lung cancer non-small cell lung carcinoma tuberculosis cancer juvenile xanthogranuloma lung carcinoma osteosarcoma familial visceral amyloidosis hypoproteinemia, hypercatabolic diffuse large B-cell lymphoma MHC class I deficiency esophageal squamous cell carcinoma kidney disease amyloidosis mature T-cell and NK-cell non-Hodgkin lymphoma autoimmune disease variant ABeta2M amyloidosis Hypergammaglobulinemia prostate cancer heart disease interstitial cystitis lung carcinoma acquired metabolic disease ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pilocytic astrocytoma psoriasis Sjogren syndrome glioblastoma juvenile dermatomyositis lung adenocarcinoma lymphatic system disease acute kidney failure pancreatic intraductal papillary-mucinous carcinoma periodic fever syndrome bone marrow disease rheumatoid arthritis Down syndrome subependymal giant cell astrocytoma lung cancer lymphoplasmacytic lymphoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm cancer schizophrenia ulcerative colitis

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.