4PP8 | pdb_00004pp8

Crystal structure of murine NK cell ligand RAE-1 beta in complex with NKG2D

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4pp8d_	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	NK cell ligand RAE-1 beta	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d4pp8c_	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	NK cell ligand RAE-1 beta	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d4pp8b_	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	C-type lectin domain	NK cell-activating receptor nkg2d	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d4pp8a_	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	C-type lectin domain	NK cell-activating receptor nkg2d	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	MHC antigen-recognition domain	8036984	3000521	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MHC antigen-recognition domain	8036984	3000521	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-type lectin-like	8033239	3001261	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C-type lectin-like	8033239	3001261	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Ribosomal_L35p	e4pp8D1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Ribosomal_L35p	ECOD (v294.1)
C	Ribosomal_L35p	e4pp8C1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Ribosomal_L35p	ECOD (v294.1)
B	Ribosomal_L35p	e4pp8B1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Ribosomal_L35p	ECOD (v294.1)
A	Ribosomal_L35p	e4pp8A1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: Ribosomal_L35p	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
C	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)
B	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
A	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	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
C, D	RAE1B	G-ALPHA1-ALPHA2-LIKE	Mus musculus (house mouse)	RAE1B*01	G-DOMAIN G-ALPHA1-LIKE, G-DOMAIN G-ALPHA2-LIKE	RPI	MH1LIKE-ALPHA-LIKE[2D]	IMGT (202611-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00059	Lectin C-type domain (Lectin_C)	Lectin C-type domain	This family includes both long and short form C-type	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Retinoic acid early-inducible protein 1-beta	natural killer cell lectin-like receptor binding protein binding binding signaling receptor binding	regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process positive regulation of cellular process regulation of macrophage activation multicellular organismal process positive regulation of macrophage activation regulation of leukocyte activation cell activation regulation of cell activation myeloid leukocyte activation leukocyte activation macrophage activation positive regulation of cell activation immune system process positive regulation of leukocyte activation positive regulation of multicellular organismal process regulation of immune system process regulation of multicellular organismal process positive regulation of immune system process response to tumor cell positive regulation of response to biotic stimulus regulation of response to biotic stimulus positive regulation of immune response to tumor cell response to stimulus immune response to tumor cell immune response regulation of immune response to tumor cell regulation of response to tumor cell response to biotic stimulus positive regulation of response to stimulus regulation of response to stimulus positive regulation of immune response regulation of immune response positive regulation of response to tumor cell lymphocyte activation positive regulation of lymphocyte activation regulation of natural killer cell activation positive regulation of natural killer cell activation natural killer cell activation regulation of lymphocyte activation regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity positive regulation of leukocyte mediated cytotoxicity positive regulation of natural killer cell mediated immunity leukocyte mediated immunity natural killer cell mediated immunity regulation of natural killer cell mediated immunity response to other organism regulation of innate immune response susceptibility to natural killer cell mediated cytotoxicity response to external stimulus leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity defense response to other organism positive regulation of defense response natural killer cell mediated cytotoxicity positive regulation of natural killer cell mediated cytotoxicity regulation of cell killing positive regulation of cell killing regulation of defense response regulation of natural killer cell mediated cytotoxicity biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of lymphocyte mediated immunity positive regulation of response to external stimulus regulation of response to stress response to stress innate immune response positive regulation of immune effector process response to external biotic stimulus positive regulation of innate immune response defense response regulation of leukocyte mediated cytotoxicity defense response to symbiont regulation of lymphocyte mediated immunity cell killing cellular response to nitrogen compound cellular response to stimulus cellular response to dsRNA cellular response to exogenous dsRNA response to dsRNA response to nitrogen compound response to exogenous dsRNA cellular response to chemical stimulus response to chemical response to lipid cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus response to bacterium cellular response to lipid response to molecule of bacterial origin antigen processing and presentation antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class Ib antigen processing and presentation of peptide antigen via MHC class Ib antigen processing and presentation via MHC class Ib adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains T cell mediated immunity positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of adaptive immune response regulation of T cell mediated immunity T cell mediated cytotoxicity positive regulation of T cell mediated cytotoxicity regulation of adaptive immune response adaptive immune response regulation of T cell mediated cytotoxicity positive regulation of T cell mediated immunity defense response to bacterium regulation of type II interferon production type II interferon production positive regulation of macromolecule biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of type II interferon production regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular region extracellular space
A, B	NKG2-D type II integral membrane protein	MHC class Ib receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity immune receptor activity binding carbohydrate binding protein binding kinase binding enzyme binding MHC class I protein binding signaling receptor binding MHC protein binding identical protein binding	regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity positive regulation of response to biotic stimulus regulation of cellular process response to stimulus response to biotic stimulus positive regulation of leukocyte mediated cytotoxicity positive regulation of immune response positive regulation of natural killer cell mediated immunity leukocyte mediated immunity regulation of immune system process natural killer cell mediated immunity positive regulation of immune system process regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity positive regulation of response to biotic stimulus regulation of cellular process response to stimulus response to biotic stimulus positive regulation of leukocyte mediated cytotoxicity positive regulation of immune response positive regulation of natural killer cell mediated immunity leukocyte mediated immunity regulation of immune system process natural killer cell mediated immunity positive regulation of immune system process regulation of biological process regulation of natural killer cell mediated immunity immune response response to other organism regulation of innate immune response response to external stimulus leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity regulation of response to stimulus defense response to other organism positive regulation of defense response natural killer cell mediated cytotoxicity regulation of immune response positive regulation of natural killer cell mediated cytotoxicity regulation of cell killing positive regulation of cell killing regulation of defense response regulation of response to biotic stimulus regulation of natural killer cell mediated cytotoxicity biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus regulation of response to stress response to stress innate immune response positive regulation of immune effector process response to external biotic stimulus positive regulation of cellular process positive regulation of innate immune response defense response regulation of leukocyte mediated cytotoxicity biological regulation defense response to symbiont regulation of lymphocyte mediated immunity immune system process cellular process cell killing regulation of biosynthetic process regulation of nitric oxide biosynthetic process reactive nitrogen species metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process developmental process cellular developmental process cell differentiation cellular response to stimulus negative regulation of mononuclear cell migration negative regulation of locomotion regulation of cell motility negative regulation of biological process negative regulation of chemotaxis regulation of lymphocyte chemotaxis natural killer cell chemotaxis taxis cell migration negative regulation of lymphocyte migration regulation of mononuclear cell migration negative regulation of cell migration chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration lymphocyte migration leukocyte migration negative regulation of leukocyte migration response to chemical regulation of locomotion negative regulation of response to external stimulus negative regulation of cell motility negative regulation of leukocyte chemotaxis regulation of natural killer cell chemotaxis lymphocyte chemotaxis regulation of lymphocyte migration regulation of cell migration negative regulation of cellular process negative regulation of lymphocyte chemotaxis cell motility locomotion cell chemotaxis negative regulation of response to stimulus regulation of chemotaxis cellular response to chemical stimulus negative regulation of immune system process negative regulation of natural killer cell chemotaxis mononuclear cell migration leukocyte chemotaxis adaptive immune response 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 response to lipid cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus response to bacterium cellular response to lipid response to molecule of bacterial origin immune response-regulating cell surface receptor signaling pathway cell communication immune response-activating signaling pathway signal transduction innate immune response-activating signaling pathway immune response-activating cell surface receptor signaling pathway response to lectin cellular response to lectin activation of innate immune response activation of immune response signaling innate immune response activating cell surface receptor signaling pathway immune response-regulating signaling pathway cell surface receptor signaling pathway stimulatory C-type lectin receptor signaling pathway multicellular organismal process cell activation natural killer cell activation lymphocyte activation leukocyte activation positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target immune response to tumor cell regulation of natural killer cell mediated cytotoxicity directed against tumor cell target regulation of natural killer cell mediated immune response to tumor cell positive regulation of immune response to tumor cell natural killer cell mediated immune response to tumor cell positive regulation of response to tumor cell positive regulation of natural killer cell mediated immune response to tumor cell regulation of response to tumor cell response to tumor cell regulation of immune response to tumor cell natural killer cell mediated cytotoxicity directed against tumor cell target regulation of type II interferon production type II interferon production positive regulation of macromolecule biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of type II interferon production regulation of gene expression positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production defense response to Gram-positive bacterium defense response to bacterium myeloid dendritic cell activation regulation of leukocyte activation positive regulation of myeloid dendritic cell activation regulation of cell activation myeloid leukocyte activation positive regulation of cell activation regulation of myeloid dendritic cell activation positive regulation of leukocyte activation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR050208	Antigen-presenting and immune regulatory MHC class I-related	Family
C, D	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
C, D	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
C, D	IPR029287	Retinoic acid early-inducible protein 1	Domain
A, B	IPR016187	C-type lectin fold	Homologous Superfamily
A, B	IPR001304	C-type lectin-like	Domain
A, B	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
A, B	IPR033992	Natural killer cell receptor-like, C-type lectin-like domain	Domain
A, B	IPR042169	NKG2-D type II integral membrane protein	Family

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.