Annotations: 3RDT

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth C]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054687	3000071	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	MHC antigen-recognition domain	8043807	3000521	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054723	3000071	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	MHC antigen-recognition domain	8043808	3000521	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 [auth C]	C1-set_2	e3rdtC2	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 [auth C]	MHC_II_alpha	e3rdtC1	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_II_alpha	ECOD (1.6)
B [auth D]	C1-set_2	e3rdtD2	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)
B [auth D]	MHC_II_alpha	e3rdtD1	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_II_alpha	ECOD (1.6)
C [auth A]	DUF1968	e3rdtA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: DUF1968	ECOD (1.6)
C [auth A]	V-set_4	e3rdtA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_4	ECOD (1.6)
D [auth B]	C1-set	e3rdtB3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
D [auth B]	V-set_3	e3rdtB4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth C]	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
A [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth D]	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
B [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth B]	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 [auth C]	MH2-AA_AB1, peptide fused to N-terminus of G-BETA	II-ALPHA	Mus musculus (house mouse)	MH2-AA	G-DOMAIN G-ALPHA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202415-0)
B [auth D]	MH2-AA_AB1, peptide fused to N-terminus of G-BETA	PEPTIDE-II-BETA	Mus musculus (house mouse)	H2-AB1*01, H2-ABb, H2-ABu	G-DOMAIN G-BETA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202415-0)
C [auth A]	TR 809.B5	TR-ALPHA	Chimeric (chimeric)	TRAV14D-3/DV802, TRAJ4501, TRAC*01	V-DOMAIN V-ALPHA, C-DOMAIN C-ALPHA	TR	TR-ALPHA_BETA-2	IMGT (202415-0)
D [auth B]	TR 809.B5	TR-BETA-2	Chimeric (chimeric)	TRBV13-201, TRBJ2-401, TRBC201, TRBC202	V-DOMAIN V-BETA, C-DOMAIN C-BETA-2	TR	TR-ALPHA_BETA-2	IMGT (202415-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
A [auth C]	PF00993	Class II histocompatibility antigen, alpha domain (MHC_II_alpha)	Class II histocompatibility antigen, alpha domain	-	Domain
B [auth D]	PF00969	Class II histocompatibility antigen, beta domain (MHC_II_beta)	Class II histocompatibility antigen, beta domain	-	Domain
B [auth D]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	H-2 class II histocompatibility antigen, A-B alpha chain	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen negative regulation of lymphocyte proliferation multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process regulation of mononuclear cell proliferation cellular process regulation of lymphocyte activation response to organic substance biological process involved in interspecies interaction between organisms response to other organism defense response response to type II interferon response to cytokine defense response to symbiont response to external stimulus response to biotic stimulus response to chemical defense response to other organism response to stress innate immune response response to external biotic stimulus peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly MHC protein complex assembly cellular component organization or biogenesis positive regulation of leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation positive regulation of leukocyte activation positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion positive regulation of multicellular organismal process regulation of leukocyte differentiation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development cell differentiation anatomical structure development T cell differentiation developmental process positive regulation of cell development leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of T cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane MHC protein complex MHC class II protein complex protein-containing complex plasma membrane protein complex membrane protein complex membrane-bounded organelle endosome membrane cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane MHC protein complex MHC class II protein complex protein-containing complex plasma membrane protein complex membrane protein complex membrane-bounded organelle 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 organelle late endosome cytoplasm vesicle organelle membrane lytic vacuole vacuole lysosome vacuolar membrane lytic vacuole membrane lysosomal membrane
B [auth D]	3K peptide, linker and MHC H-2 class II I-Ab beta chain	protein antigen binding protein binding binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding toxic substance binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process multicellular organismal process regulation of cellular process regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process multicellular organismal process regulation of cellular process regulation of leukocyte activation regulation of alpha-beta T cell 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 alpha-beta T cell activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation positive regulation of alpha-beta T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process cellular process regulation of lymphocyte activation positive regulation of T-helper 1 type immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of adaptive immune response T-helper 1 type immune response adaptive immune response regulation of T-helper 1 type immune response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen lymphocyte mediated immunity immunoglobulin production cellular developmental process immunoglobulin production involved in immunoglobulin-mediated immune response cellular biosynthetic process cell development mononuclear cell differentiation B cell affinity maturation lymphocyte differentiation organic substance metabolic process B cell differentiation cell differentiation organic substance biosynthetic process anatomical structure development leukocyte mediated immunity production of molecular mediator of immune response developmental process hemopoiesis cellular metabolic process B cell activation gene expression immunoglobulin mediated immune response macromolecule biosynthetic process immune effector process biosynthetic process peripheral B cell selection B cell mediated immunity B cell selection metabolic process macromolecule metabolic process leukocyte differentiation peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly MHC protein complex assembly cellular component organization or biogenesis cellular response to stimulus response to organic substance biological process involved in interspecies interaction between organisms response to type II interferon response to cytokine cellular response to type II interferon response to biotic stimulus response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus cellular response to organic substance response to other organism defense response defense response to symbiont response to external stimulus cellular response to chemical stimulus response to chemical defense response to other organism regulation of antigen processing and presentation positive regulation of antigen processing and presentation	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane MHC protein complex MHC class II protein complex protein-containing complex plasma membrane protein complex membrane protein complex membrane-bounded organelle endosome membrane cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane MHC protein complex MHC class II protein complex protein-containing complex plasma membrane protein complex membrane protein complex membrane-bounded organelle 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 organelle late endosome cytoplasm vesicle organelle membrane multivesicular body early endosome vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi apparatus
C [auth A]	TCR 809.B5 alpha chain	-	-	-
D [auth B]	TCR 809.B5 beta chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth C]	IPR003597	Immunoglobulin C1-set	Domain
A [auth C]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A [auth C]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth C]	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
A [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth C]	IPR007110	Immunoglobulin-like domain	Domain
A [auth C]	IPR001003	MHC class II, alpha chain, N-terminal	Domain
B [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth D]	IPR003597	Immunoglobulin C1-set	Domain
B [auth D]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
B [auth D]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B [auth D]	IPR000353	MHC class II, beta chain, N-terminal	Domain
B [auth D]	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
B [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth D]	IPR007110	Immunoglobulin-like domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.