3RDT | pdb_00003rdt

Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth B]		e3rdtB3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: V-set	F:	ECOD (20:10:01)
C [auth A]		e3rdtA1	A: OB-fold	X: RIFT-related	H: Phage tail proteins	T: H2TH	F:	ECOD (20:10:01)
B [auth D]		e3rdtD1	A: SSHS domain	X: His-Me finger endonucleases	H: His-Me finger endonucleases	T:	F:	ECOD (20:10:01)
A [auth C]		e3rdtC1	A: SSHS domain	X: His-Me finger endonucleases	H: His-Me finger endonucleases	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	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)
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)
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)

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 [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 (202609-0)
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 (202609-0)
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 (202609-0)
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 (202609-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D]	IPR000353	MHC class II, beta chain, N-terminal	Domain
B [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth D]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B [auth D]	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
B [auth D]	IPR003597	Immunoglobulin C1-set	Domain
B [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth D]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
B [auth D]	IPR007110	Immunoglobulin-like domain	Domain
B [auth D]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth C]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
A [auth C]	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
A [auth C]	IPR003597	Immunoglobulin C1-set	Domain
A [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth C]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A [auth C]	IPR007110	Immunoglobulin-like domain	Domain
A [auth C]	IPR001003	MHC class II, alpha chain, N-terminal	Domain
A [auth C]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

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.