3DMM

Crystal structure of the CD8 alpha beta/H-2Dd complex

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)
B	d3dmmb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	beta2-microglobulin	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3dmmb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054617	3000071	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8055650	3000521	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054571	3000071	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054489	3000071	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054491	3000071	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)
A	C1-set_2	e3dmmA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
A	MHC_I	e3dmmA2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_I	ECOD (1.6)
B	C1-set_2	e3dmmB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
D [auth C]	I-set_12	e3dmmC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_12	ECOD (1.6)
E [auth D]	V-set_5	e3dmmD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth D]	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	MH1-D1*02	I-ALPHA	Mus musculus (house mouse)	H2-D1*02	G-DOMAIN G-ALPHA1, G-DOMAIN G-ALPHA2, C-LIKE-DOMAIN C-LIKE	MH	MH1-ALPHA_B2M	IMGT (202450-0)
B	MH1-D1*02	B2M	Mus musculus (house mouse)	B2M*01	C-LIKE-DOMAIN C-LIKE	MH	MH1-ALPHA_B2M	IMGT (202450-0)
D [auth C]	CD8A_CD8B homodimer	1V-LIKE	Mus musculus (house mouse)	CD8A*02	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE_1V-LIKE	IMGT (202450-0)
E [auth D]	CD8A_CD8B homodimer	1V-LIKE	Mus musculus (house mouse)	CD8B*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE_1V-LIKE	IMGT (202450-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00129	Class I Histocompatibility antigen, domains alpha 1 and 2 (MHC_I)	Class I Histocompatibility antigen, domains alpha 1 and 2	-	Domain
A	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
D [auth C]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
E [auth D]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	H-2 class I histocompatibility antigen, D-D alpha chain	-	antigen processing and presentation immune system process 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-dependent 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 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 response to stimulus antigen processing and presentation immune system process 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-dependent 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 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 response to stimulus immune response leukocyte mediated cytotoxicity adaptive immune response immune effector process leukocyte mediated immunity cellular process cell killing regulation of immune effector process 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 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 regulation of biological process positive regulation of T cell mediated cytotoxicity regulation of adaptive immune response biological regulation regulation of 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 regulation of neuron projection development multicellular organismal process 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	membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane lumenal side of endoplasmic reticulum membrane intracellular membrane-bounded organelle endomembrane system side of membrane lumenal side of membrane endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network membrane-bounded organelle intracellular anatomical structure organelle subcompartment membrane lumenal side of endoplasmic reticulum membrane intracellular membrane-bounded organelle endomembrane system side of membrane lumenal side of membrane endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane intracellular vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane vesicle endocytic vesicle cell periphery cell surface plasma membrane external side of plasma membrane MHC class I protein complex MHC protein complex protein-containing complex plasma membrane protein complex membrane protein complex
B	Beta-2 microglobulin	identical protein binding protein binding 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 protein refolding primary metabolic process gene expression macromolecule biosynthetic process 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 cellular process protein metabolic process macromolecule metabolic process localization transport iron ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport 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 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 regulation of macromolecule biosynthetic 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 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 system process sensory perception of chemical stimulus sensory perception nervous system process sensory perception of smell cellular component organization cellular component organization or biogenesis supramolecular fiber organization amyloid fibril formation cellular response to stimulus cellular response to iron(III) ion cellular response to metal ion response to iron(III) ion cellular response to iron ion cellular response to chemical stimulus response to metal ion response to iron ion response to chemical protein-containing complex organization protein homotetramerization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization multicellular organismal-level iron ion homeostasis multicellular organismal-level homeostasis multicellular organismal-level chemical homeostasis T cell mediated cytotoxicity leukocyte mediated cytotoxicity cell killing 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 neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process 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 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 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 peptide antigen antigen processing and presentation of exogenous antigen cell activation mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation T cell differentiation leukocyte differentiation cellular response to nicotine response to nicotine regulation of localization import into cell positive regulation of cellular component organization vesicle-mediated transport 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 positive regulation of transport endocytosis receptor-mediated endocytosis 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 peptide antigen via MHC class I antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I behavior learning or memory cognition peptide antigen assembly with MHC class I protein complex peptide antigen assembly with MHC protein complex MHC class I protein complex assembly MHC protein complex assembly defense response cellular defense response 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 positive regulation of leukocyte mediated cytotoxicity positive regulation of T cell mediated cytotoxicity regulation of leukocyte mediated cytotoxicity regulation of T cell mediated cytotoxicity regulation of cell killing positive regulation of cell killing 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 protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex HFE-transferrin receptor complex receptor complex intracellular anatomical structure cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex HFE-transferrin receptor complex receptor complex intracellular anatomical structure cytoplasm cytosol MHC class I protein complex MHC protein complex membrane-bounded organelle intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane vesicle organelle membrane endocytic vesicle Golgi apparatus endomembrane system MHC class I peptide loading complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane extracellular region extracellular space
C [auth P]	Synthetic peptide	-	-	-
D [auth C]	T-cell surface glycoprotein CD8 alpha chain	identical protein binding protein binding binding	multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling positive regulation of calcium-mediated signaling signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling regulation of cell communication positive regulation of signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated immunity immune response leukocyte mediated immunity adaptive immune response immune effector process cell surface receptor signaling pathway immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway regulation of immune response antigen receptor-mediated signaling pathway activation of immune response developmental process cytotoxic T cell differentiation cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation cell differentiation anatomical structure development T cell differentiation leukocyte differentiation biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus	protein-containing complex receptor complex cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane
E [auth D]	T-cell surface glycoprotein CD8 beta chain	molecular transducer activity coreceptor activity signaling receptor activity protein binding binding MHC class I protein binding signaling receptor binding MHC protein binding	multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response biological regulation T cell receptor signaling pathway regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response adaptive immune response	protein-containing complex receptor complex 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
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR050208	Antigen-presenting and immune regulatory MHC class I-related	Family
A	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
A	IPR003597	Immunoglobulin C1-set	Domain
A	IPR010579	MHC class I, alpha chain, C-terminal	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR011161	MHC class I-like antigen recognition-like	Domain
A	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR001039	MHC class I alpha chain, alpha1 alpha2 domains	Domain
A	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B	IPR003597	Immunoglobulin C1-set	Domain
B	IPR015707	Beta-2-Microglobulin	Family
B	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR007110	Immunoglobulin-like domain	Domain
D [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth C]	IPR015468	CD8 alpha subunit	Family
D [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth C]	IPR013106	Immunoglobulin V-set domain	Domain
D [auth C]	IPR003599	Immunoglobulin domain subtype	Domain
D [auth C]	IPR007110	Immunoglobulin-like domain	Domain
E [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth D]	IPR042414	T-cell surface glycoprotein CD8 beta chain	Family
E [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth D]	IPR013106	Immunoglobulin V-set domain	Domain
E [auth D]	IPR003599	Immunoglobulin domain subtype	Domain
E [auth D]	IPR007110	Immunoglobulin-like domain	Domain