1IM9 | pdb_00001im9

Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1 bound to its MHC ligand HLA-Cw4

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1im9d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	Killer cell inhibitory receptor	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1im9f2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	beta2-microglobulin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1im9f3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1im9b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	beta2-microglobulin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1im9b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1im9e1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class I MHC, alpha-3 domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1im9e2	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	Class I MHC, alpha-1 and alpha-2 domains	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1im9a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class I MHC, alpha-3 domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1im9a2	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	Class I MHC, alpha-1 and alpha-2 domains	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Copper-bind	e1im9D1	A: alpha arrays	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Copper-bind	ECOD (v295.2)
F	Copper-bind	e1im9F1	A: alpha arrays	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Copper-bind	ECOD (v295.2)
B	Copper-bind	e1im9B1	A: alpha arrays	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Copper-bind	ECOD (v295.2)
E	Copper-bind	e1im9E1	A: alpha arrays	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Copper-bind	ECOD (v295.2)
E	Anthrax_toxA	e1im9E2	A: alpha arrays	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Anthrax_toxA	ECOD (v295.2)
A	Copper-bind	e1im9A1	A: alpha arrays	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Copper-bind	ECOD (v295.2)
A	Anthrax_toxA	e1im9A2	A: alpha arrays	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Anthrax_toxA	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
A	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
D	KIR2DL1	2C-LIKE	Homo sapiens (human)	KIR2DL1*0040101	C-LIKE-DOMAIN C-LIKE	RPI-KIR	2C-LIKE	IMGT (202640-0)
B, F	MH1 HLA-C*0401	B2M	Homo sapiens (human)	B2M01, B2M02	C-LIKE-DOMAIN C-LIKE	MH	MH1-ALPHA_B2M	IMGT (202640-0)
A, E	MH1 HLA-C*0401	I-ALPHA	Homo sapiens (human)	HLA-C0401, HLA-C0430, HLA-C*0433	G-DOMAIN G-ALPHA1, G-DOMAIN G-ALPHA2, C-LIKE-DOMAIN C-LIKE	MH	MH1-ALPHA_B2M	IMGT (202640-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF00047	Immunoglobulin domain (ig)	Immunoglobulin domain	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prote ...	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.	Domain
B, F	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A, E	PF00129	Class I Histocompatibility antigen, domains alpha 1 and 2 (MHC_I)	Class I Histocompatibility antigen, domains alpha 1 and 2		Domain
A, E	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
D	KILLER CELL IMMUNOGLOBULIN-LIKE RECEPTOR 2DL1	molecular transducer activity signaling receptor activity immune receptor activity transmembrane signaling receptor activity	cellular response to stimulus regulation of biological process immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling immune response biological regulation cell communication immune response-inhibiting cell surface receptor signaling pathway immune response-regulating signaling pathway regulation of response to stimulus immune system process immune response-inhibiting signal transduction cellular response to stimulus regulation of biological process immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling immune response biological regulation cell communication immune response-inhibiting cell surface receptor signaling pathway immune response-regulating signaling pathway regulation of response to stimulus immune system process immune response-inhibiting signal transduction regulation of immune response cellular process regulation of immune system process signal transduction natural killer cell inhibitory signaling pathway	cell periphery cellular anatomical structure plasma membrane membrane
C, G	HLA-Cw4-specific peptide	-	-	-
B, F	Beta-2 microglobulin	binding 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	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 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity 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 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process response to stimulus T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of immune response cytokine production leukocyte mediated immunity regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production positive regulation of immune system process regulation of T cell mediated immunity regulation of biological process regulation of cytokine production involved in immune response immune response regulation of adaptive immune response immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process regulation of response to stimulus positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process regulation of immune response metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic 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 T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process regulation of multicellular organismal process cytokine production involved in immune response positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process adaptive immune response regulation of lymphocyte mediated immunity positive regulation of gene expression immune system process positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response cellular process 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 regulation of localization import into cell regulation of cellular component organization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis vesicle-mediated transport cellular component organization localization negative regulation of cellular process cellular component organization or biogenesis regulation of endocytosis negative regulation of cellular component organization negative regulation of receptor-mediated endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis positive regulation of cellular component organization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis positive regulation of transport 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 antigen processing and presentation cellular component assembly protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class I MHC protein complex assembly antigen processing and presentation of peptide antigen regulation of developmental process cellular developmental process cell development regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of nervous system development negative regulation of neurogenesis multicellular organism development neurogenesis cell differentiation anatomical structure development negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development negative regulation of developmental process nervous system development negative regulation of cell development negative regulation of multicellular organismal process animal gross anatomical part developmental process regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus response to biotic stimulus response to stress regulation of response to stress innate immune response response to external biotic stimulus natural killer cell mediated immunity regulation of natural killer cell mediated immunity response to other organism defense response regulation of innate immune response defense response to symbiont response to external stimulus defense response to other organism antigen processing and presentation of peptide antigen via MHC class Ib antigen processing and presentation via MHC class Ib 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 exogenous antigen 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 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 primary metabolic process protein metabolic process 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 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 antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I behavior learning or memory cognition negative regulation of monoatomic ion transport regulation of monoatomic ion transport regulation of iron ion transport regulation of metal ion transport negative regulation of iron ion transport regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation 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 cell activation 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 neuron differentiation head development forebrain generation of neurons animal organ development brain development generation of neurons central nervous system development forebrain neuron differentiation negative regulation of neuron differentiation regulation of neuron differentiation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex signaling receptor complex HFE-transferrin receptor complex MHC class I protein complex MHC protein complex endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome cytoplasm organelle membrane MHC class Ib protein complex phagocytic vesicle phagocytic vesicle membrane endocytic vesicle membrane endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi apparatus membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen endoplasmic reticulum 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
A, E	HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, CW-4 CW*0401 ALPHA CHAIN	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D	IPR003599	Immunoglobulin domain subtype	Domain
D	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
D	IPR050412	Immunoglobulin-like Receptors in Immune Regulation	Family
B, F	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, F	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, F	IPR007110	Immunoglobulin-like domain	Domain
B, F	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B, F	IPR003597	Immunoglobulin C1-set	Domain
B, F	IPR015707	Beta-2-Microglobulin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	: P43626	osteosarcoma ovarian cancer psoriasis
B, F	: P61769	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 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 ovarian cancer acquired metabolic disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pilocytic astrocytoma psoriasis Sjogren syndrome glioblastoma juvenile dermatomyositis lung adenocarcinoma lymphatic system disease pancreatic intraductal papillary-mucinous carcinoma acute kidney failure 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