4H25

TCR interaction with peptide mimics of nickel offers structure insights to nickel contact allergy

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4h25a2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC alpha chain, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4h25a1	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	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4h25d2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC alpha chain, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4h25d1	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	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4h25b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4h25b1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4h25b4	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4h25b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4h25e2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4h25e1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4h25e4	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4h25e3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8040455	3000521	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054671	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054671	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MHC antigen-recognition domain	8040455	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	C1-set_2	e4h25A1	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_II_alpha	e4h25A2	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)
D	C1-set_2	e4h25D1	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	MHC_II_alpha	e4h25D2	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	C1-set_2	e4h25B1	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	MHC_II_beta	e4h25B2	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_beta	ECOD (1.6)
E	C1-set_2	e4h25E1	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)
E	MHC_II_beta	e4h25E2	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_beta	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
D	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
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)
E	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
E	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, D	Major histocompatibility II (MH2)	II-ALPHA	Homo sapiens (human)	HLA-DRA0101, HLA-DRA0102	G-DOMAIN G-ALPHA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_BETA	IMGT (202415-0)
B, E	Major histocompatibility II (MH2)	II-BETA	Homo sapiens (human)	HLA-DRB3*0301	G-DOMAIN G-BETA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_BETA	IMGT (202415-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
A, D	PF00993	Class II histocompatibility antigen, alpha domain (MHC_II_alpha)	Class II histocompatibility antigen, alpha domain	-	Domain
B, E	PF00969	Class II histocompatibility antigen, beta domain (MHC_II_beta)	Class II histocompatibility antigen, beta domain	-	Domain
B, E	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, D	HLA class II histocompatibility antigen, DR alpha chain	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity MHC class II receptor activity immune receptor activity polysaccharide binding carbohydrate binding binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity MHC class II receptor activity immune receptor activity polysaccharide binding carbohydrate binding protein binding signaling receptor binding T cell receptor binding	multicellular organismal process regulation of cellular process regulation of alpha-beta T cell activation regulation of leukocyte 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 CD4-positive, alpha-beta T cell activation positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion multicellular organismal process regulation of cellular process regulation of alpha-beta T cell activation regulation of leukocyte 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 CD4-positive, alpha-beta T cell activation positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation CD4-positive, alpha-beta 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 CD4-positive, alpha-beta T cell activation immune system process regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process cellular process regulation of lymphocyte activation response to stimulus immune response positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus regulation of immune response antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of endogenous peptide antigen via MHC class II antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of exogenous antigen system process nervous system process cognition 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 dendritic cell antigen processing and presentation myeloid dendritic cell antigen processing and presentation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity positive regulation of leukocyte mediated immunity positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of leukocyte mediated cytotoxicity leukocyte mediated immunity positive regulation of immune effector process 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 regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity regulation of T cell mediated cytotoxicity regulation of lymphocyte mediated immunity positive regulation of T cell mediated immunity regulation of cell killing positive regulation of cell killing cell killing regulation of leukocyte differentiation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation involved in immune response alpha-beta T cell differentiation involved in immune response regulation of cell development multicellular organism development cell differentiation regulation of T-helper cell differentiation anatomical structure development T cell differentiation developmental process T-helper cell differentiation leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation regulation of T cell differentiation alpha-beta T cell differentiation T cell activation involved in immune response alpha-beta T cell activation involved in immune response leukocyte activation involved in immune response lymphocyte activation involved in immune response regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis T cell differentiation involved in immune response regulation of hemopoiesis immunological memory formation process positive regulation of T cell differentiation positive regulation of developmental process positive regulation of memory T cell differentiation positive regulation of cell development memory T cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of memory T cell differentiation immunological memory process positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation positive regulation of CD4-positive, alpha-beta T cell differentiation positive regulation of regulatory T cell differentiation regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation positive regulation of alpha-beta T cell differentiation positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation regulation of regulatory T cell differentiation CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation regulatory T cell differentiation	membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane membrane cellular anatomical entity intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell surface MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex endosome membrane endosome late endosome membrane endomembrane system late endosome lytic vacuole vacuole lysosome organelle subcompartment lumenal side of endoplasmic reticulum membrane side of membrane lumenal side of membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane immunological synapse vacuolar membrane lytic vacuole membrane lysosomal membrane Golgi membrane Golgi apparatus early endosome early endosome membrane autolysosome autolysosome membrane secondary lysosome Golgi apparatus subcompartment trans-Golgi network membrane trans-Golgi network transport vesicle transport vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane
B, E	MHC class II antigen	-	antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II immune system process response to stimulus immune response adaptive immune response	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex endosome membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle
C, F	peptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D	Pharos: P01903	lung carcinoma toxic shock syndrome multiple sclerosis juvenile dermatomyositis systemic sclerosis ulcerative colitis Parkinson disease Sjogren syndrome Crohn disease pancreatic ductal adenocarcinoma Graham Little Piccardi Lassueur syndrome pilocytic astrocytoma Hashimoto thyroiditis psoriatic arthritis Hodgkins lymphoma lung carcinoma toxic shock syndrome multiple sclerosis juvenile dermatomyositis systemic sclerosis ulcerative colitis Parkinson disease Sjogren syndrome Crohn disease pancreatic ductal adenocarcinoma Graham Little Piccardi Lassueur syndrome pilocytic astrocytoma Hashimoto thyroiditis psoriatic arthritis Hodgkins lymphoma invasive ductal breast carcinoma skin basal cell carcinoma limb-girdle muscular dystrophy systemic lupus erythematosus adrenal cortex carcinoma astrocytic tumor malignant glioma Becker muscular dystrophy celiac disease neoplasm of mature B-cells dermatomyositis non-alcoholic fatty liver disease Down syndrome osteoporosis esophageal adenocarcinoma pancreatic intraductal papillary-mucinous carcinoma Graham Little-Piccardi-Lassueur syndrome primary biliary cholangitis head and neck cancer IgA glomerulonephritis squamous cell lung carcinoma lung adenocarcinoma lymphoplasmacytic lymphoma atopic eczema marginal zone lymphoma breast cancer chronic obstructive pulmonary disease nephrotic syndrome diabetes mellitus non-small cell lung carcinoma Duchenne muscular dystrophy ovarian cancer glioblastoma Graves disease prostate carcinoma heart disease interstitial cystitis juvenile idiopathic arthritis subependymal giant cell astrocytoma lung cancer temporal arteritis alopecia areata malignant ependymoma vitiligo autism spectrum disorder membranous glomerulonephritis breast carcinoma myasthenia gravis nodular sclerosis classical Hodgkin lymphoma diffuse scleroderma osteoarthritis

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.