3DI3

Crystal structure of the complex of human interleukin-7 with glycosylated human interleukin-7 receptor alpha ectodomain

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	PF01415	e3di3A1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: PF01415	ECOD (1.6)
B	PF00041	e3di3B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00041	ECOD (1.6)
B	PF18447	e3di3B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF18447	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1250.50	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
B	2.60.40.1870	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01415	Interleukin 7 (IL7)	Interleukin 7	IL-7 is a cytokine that acts as a growth factor for early lymphoid cells of both B- and T-cell lineages. IL-7 and IL-7Ralpha bind the gamma-c receptor forming a complex crucial to several signaling cascades leading to the development and homeostasis ...	IL-7 is a cytokine that acts as a growth factor for early lymphoid cells of both B- and T-cell lineages. IL-7 and IL-7Ralpha bind the gamma-c receptor forming a complex crucial to several signaling cascades leading to the development and homeostasis of T and B cells [1] [2].	Domain
B	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain	-	Domain
B	PF18447	Fibronectin type III domain (FN3_7)	Fibronectin type III domain	This domain is found in Interleukin-7 receptor subunit alpha (IL-7Ralpha), which together IL-7 form a complex crucial to several signalling cascades leading to the development and homeostasis of T and B cells. IL-7Ralpha carries a 219 residue ectodom ...	This domain is found in Interleukin-7 receptor subunit alpha (IL-7Ralpha), which together IL-7 form a complex crucial to several signalling cascades leading to the development and homeostasis of T and B cells. IL-7Ralpha carries a 219 residue ectodomain on the N-terminal region which is crucial for T and B-cell development. Mutations in the IL-7Ralpha ectodomain inhibits T and B cell development, resulting in patients with a form of severe combined immunodeficiency (SCID). The ectodomain folds into two fibronectin type III (FNIII) domains connected by a 310-helical linker. This entry comprises the first of the two FNIII domains, D1 while D2 domain is Pfam:PF00041. In the D1 domain of IL-7Ralpha, a disulfide bond (C22R-C37R) conserved among cytokine receptor class I (CRH I) family members bridges two beta strands [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Interleukin-7	protein binding binding signaling receptor binding cytokine receptor binding growth factor receptor binding interleukin-7 receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity cytokine activity	cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular process cellular response to organic substance signal transduction negative regulation of extrinsic apoptotic signaling pathway in absence of ligand signal transduction in absence of ligand negative regulation of signaling negative regulation of biological process regulation of signal transduction regulation of programmed cell death negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand regulation of signaling negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway developmental process multicellular organismal process developmental growth growth organ growth anatomical structure morphogenesis animal organ development anatomical structure development animal organ morphogenesis multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells humoral immune response immune response immune system process regulation of protein modification process regulation of protein phosphorylation peptidyl-tyrosine modification regulation of primary metabolic process organic substance metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process organonitrogen compound metabolic process protein phosphorylation phosphorylation cellular metabolic process regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process peptidyl-tyrosine phosphorylation regulation of metabolic process cell-cell signaling positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process positive regulation of response to cytokine stimulus positive regulation of response to stimulus positive regulation of cellular process regulation of cytokine-mediated signaling pathway regulation of response to cytokine stimulus positive regulation of cytokine-mediated signaling pathway positive regulation of signaling cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation mononuclear cell proliferation lymphocyte proliferation cellular developmental process hemopoiesis cell development mononuclear cell differentiation T cell lineage commitment lymphocyte differentiation T cell activation cell differentiation T cell differentiation cell fate commitment leukocyte differentiation cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production organic substance biosynthetic process cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of biosynthetic process gene expression macromolecule biosynthetic process regulation of chemokine production regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression chemokine production positive regulation of chemokine production positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production positive regulation of cellular biosynthetic process regulation of growth regulation of developmental growth regulation of developmental process positive regulation of organ growth positive regulation of developmental process positive regulation of growth regulation of organ growth positive regulation of developmental growth positive regulation of B cell proliferation regulation of leukocyte activation regulation of cell activation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of immune system process positive regulation of immune system process 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 regulation of leukocyte differentiation regulation of cell differentiation positive regulation of B cell differentiation regulation of cell development multicellular organism development positive regulation of cell development regulation of B cell differentiation B cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation tissue remodeling bone remodeling bone resorption positive regulation of T cell differentiation positive regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of T cell differentiation cell adhesion cell-cell adhesion regulation of cell-cell adhesion positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation	cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity extracellular region extracellular space
B	Interleukin-7 receptor subunit alpha	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity interleukin-7 receptor activity cytokine receptor activity immune receptor activity binding antigen binding	cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular process cellular response to organic substance signal transduction developmental process immune system development multicellular organism development multicellular organismal process lymph node development immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development immune response regulation of DNA recombination DNA recombination primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA metabolic process positive regulation of cell communication cell surface receptor signaling pathway via STAT positive regulation of signal transduction positive regulation of biological process positive regulation of receptor signaling pathway via STAT regulation of signal transduction positive regulation of response to stimulus positive regulation of cellular process regulation of signaling regulation of response to stimulus regulation of cell communication regulation of receptor signaling pathway via STAT positive regulation of signaling cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process regulation of cellular 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 positive regulation of cellular biosynthetic process cellular component organization regulation of cellular component size cellular component organization or biogenesis regulation of biological quality regulation of cell size regulation of anatomical structure size multicellular organismal-level homeostasis leukocyte homeostasis T cell homeostasis homeostatic process homeostasis of number of cells lymphocyte homeostasis cellular developmental process hemopoiesis cell differentiation cell development B cell homeostasis regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development T cell differentiation in thymus positive regulation of developmental process positive regulation of cell activation positive regulation of T cell differentiation in thymus T cell activation positive regulation of leukocyte activation T cell differentiation regulation of immune system process positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process leukocyte differentiation regulation of developmental process positive regulation of leukocyte cell-cell adhesion regulation of T cell differentiation in thymus lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation regulation of multicellular organismal process regulation of cell-cell adhesion regulation of lymphocyte differentiation regulation of multicellular organismal development positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains T cell mediated cytotoxicity lymphocyte mediated immunity T cell mediated immunity leukocyte mediated cytotoxicity adaptive immune response immune effector process leukocyte mediated immunity cell killing cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation B cell activation B cell proliferation leukocyte proliferation mononuclear cell proliferation lymphocyte proliferation regulation of immune effector process negative regulation of biological process negative regulation of lymphocyte mediated immunity regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains negative regulation of leukocyte mediated cytotoxicity negative regulation of cellular process negative regulation of cell killing regulation of T cell mediated immunity regulation of adaptive immune response negative regulation of response to stimulus negative regulation of immune response negative regulation of T cell mediated cytotoxicity negative regulation of immune effector process regulation of leukocyte mediated cytotoxicity negative regulation of adaptive immune response negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte mediated immunity regulation of T cell mediated cytotoxicity regulation of lymphocyte mediated immunity negative regulation of immune system process regulation of immune response regulation of cell killing negative regulation of leukocyte mediated immunity negative regulation of T cell mediated immunity anatomical structure morphogenesis cell morphogenesis positive regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via JAK-STAT cell surface receptor signaling pathway via JAK-STAT regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process negative regulation of programmed cell death leukocyte apoptotic process regulation of apoptotic process regulation of programmed cell death cell death negative regulation of T cell apoptotic process lymphocyte apoptotic process negative regulation of apoptotic process negative regulation of leukocyte apoptotic process regulation of T cell apoptotic process T cell apoptotic process apoptotic process programmed cell death negative regulation of lymphocyte apoptotic process biological process involved in interspecies interaction between organisms response to other organism defense response defense response to Gram-positive bacterium response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018049	Interleukin-7/Interleukin-9, conserved site	Conserved Site
A	IPR001181	Interleukin-7	Family
A	IPR038325	Interleukin-7 superfamily	Homologous Superfamily
B	IPR003531	Short hematopoietin receptor, family 1, conserved site	Conserved Site
B	IPR003961	Fibronectin type III	Domain
B	IPR040997	IL-7Ralpha, fibronectin type III domain	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P13232	lymphopenia multiple sclerosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia adult acute respiratory distress syndrome Brain Injuries, Focal breast cancer Crohn disease lymphatic system disease malignant glioma pilocytic astrocytoma autoimmune disease brain injury cancer glioblastoma lung cancer lymphopenia multiple sclerosis pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia adult acute respiratory distress syndrome Brain Injuries, Focal breast cancer Crohn disease lymphatic system disease malignant glioma pilocytic astrocytoma autoimmune disease brain injury cancer glioblastoma lung cancer malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm sarcoidosis COVID-19 HIV infectious disease lung carcinoma malignant colon neoplasm
B	Pharos: P16871	ulcerative colitis Omenn syndrome primary biliary cholangitis severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive multiple sclerosis Precursor T-Cell Lymphoblastic Leukemia-Lymphoma endometriosis atopic eczema severe combined immunodeficiency lung adenocarcinoma malignant glioma non-small cell lung carcinoma ovarian cancer acute myeloid leukemia asthma ulcerative colitis Omenn syndrome primary biliary cholangitis severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive multiple sclerosis Precursor T-Cell Lymphoblastic Leukemia-Lymphoma endometriosis atopic eczema severe combined immunodeficiency lung adenocarcinoma malignant glioma non-small cell lung carcinoma ovarian cancer acute myeloid leukemia asthma sarcoidosis B-cell chronic lymphocytic leukemia Sjogren syndrome breast cancer cutaneous lupus erythematosus interstitial cystitis lung cancer malignant mesothelioma multiple sclerosis, susceptibility to, 3 pituitary cancer acute T cell leukemia tuberculosis cancer cystic fibrosis gastric carcinoma lung carcinoma osteosarcoma allergic rhinitis psoriasis autoimmune disease Hashimoto thyroiditis

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.