3CUP | pdb_00003cup

Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235

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)
A	d3cupa2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC alpha chain, C-terminal domain	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3cupa1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	Class II MHC alpha chain, N-terminal domain	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3cupa3	Artifacts	Tags	Tags	Tags	C-terminal Tags	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)
B	SCOP2B Superfamily	MHC antigen-recognition domain	8055622	3000521	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054689	3000071	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8034745	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)
B	Topoisom_bac	e3cupB1	A: a/b three-layered sandwiches	X: YrdC/RibB	H: SH3	T: SH3	F: Topoisom_bac	ECOD (v294.1)
B	Cas9_PI2	e3cupB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: Cas9_PI2	ECOD (v294.1)
A	MHC_II_alpha	e3cupA1	A: a/b three-layered sandwiches	X: TAZ domain	H: TAZ domain	T: Lipocalins	F: MHC_II_alpha	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, 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
B	pMHC-II, MH2-AAd_MH2-ABd	PEPTIDE-II-BETA	Mus musculus (house mouse)	H2-AB-NOD	G-DOMAIN G-BETA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202612-0)
A	pMHC-II, MH2-AAd_MH2-ABd	II-ALPHA	Mus musculus (house mouse)	MH2-AAd	G-DOMAIN G-ALPHA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202612-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A	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
B	MHC class II H2-IA-beta chain linked to GAD221-235 peptide	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding glutamate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity protein-containing complex binding vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding glutamate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity protein-containing complex binding organic acid binding amino acid binding carboxylic acid binding glutamate binding	response to stimulus response to chemical response to xenobiotic stimulus small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process GABA metabolic process carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process amino acid biosynthetic process response to stimulus response to chemical response to xenobiotic stimulus small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process GABA metabolic process carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process GABA biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process non-proteinogenic amino acid biosynthetic process response to ketone response to lipid response to hormone response to steroid hormone response to endogenous stimulus response to progesterone response to oxygen-containing compound cellular response to endogenous stimulus cellular response to growth factor stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor response to decreased oxygen levels cellular response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to oxygen levels response to abiotic stimulus dicarboxylic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process succinate metabolic process proteinogenic amino acid metabolic process GABA shunt glutamate metabolic process response to nutrient levels response to caloric restriction response to glucocorticoid response to corticosteroid response to dexamethasone trans-synaptic signaling synaptic signaling regulation of biological process signaling anterograde trans-synaptic signaling biological regulation cell-cell signaling chemical synaptic transmission cell communication response to nitrogen compound response to cocaine response to alkaloid immune response 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery presynapse synapse cell junction membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane GABA-ergic synapse cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery presynapse synapse cell junction membrane plasma membrane presynaptic membrane plasma membrane region synaptic membrane GABA-ergic synapse membrane-bounded organelle Golgi membrane Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle organelle membrane perinuclear region of cytoplasm somatodendritic compartment cell body neuronal cell body intracellular vesicle transport vesicle membrane cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle exocytic vesicle axon cell projection neuron projection plasma membrane bounded cell projection inhibitory synapse early endosome endosome cell surface MHC protein complex MHC class II protein complex protein-containing complex plasma membrane protein complex membrane protein complex late endosome multivesicular body
A	H-2 class II histocompatibility antigen, A-D alpha chain	binding antigen binding peptide antigen binding peptide binding	response to stimulus immune response 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 multicellular organismal process regulation of leukocyte differentiation regulation of cellular process response to stimulus immune response 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 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	IPR002129	Pyridoxal phosphate-dependent decarboxylase, major domain	Domain
B	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
B	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
B	IPR021115	Pyridoxal-phosphate binding site	Binding Site
B	IPR000353	MHC class II, beta chain, N-terminal	Domain
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
B	IPR003597	Immunoglobulin C1-set	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
B	IPR007110	Immunoglobulin-like domain	Domain
B	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
A	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
A	IPR003597	Immunoglobulin C1-set	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR001003	MHC class II, alpha chain, N-terminal	Domain
A	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site