3QIB

Crystal structure of the 2B4 TCR in complex with MCC/I-Ek

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3qiba2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3qiba1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3qibb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC beta chain, C-terminal domain	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3qibb1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	Class II MHC beta chain, N-terminal domain	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3qibc2	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)
C	d3qibc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3qibd2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3qibd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(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	8054673	3000071	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8033118	3000521	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MHC antigen-recognition domain	8055626	3000521	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054547	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	e3qibA1	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	e3qibA2	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	e3qibB2	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	e3qibB3	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)
C	DUF1968	e3qibC2	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	V-set_4	e3qibC1	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	C1-set	e3qibD3	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	V-set_3	e3qibD4	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	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)
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)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
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	MH2-EAk_MH2-EB1k, peptide fused to N-terminus of G-BETA	II-ALPHA	Mus musculus (house mouse)	MH2-AAe, H2-EAck, H2-EAk, H2-EA	G-DOMAIN G-ALPHA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202436-0)
B	MH2-EAk_MH2-EB1k, peptide fused to N-terminus of G-BETA	PEPTIDE-II-BETA	Mus musculus (house mouse)	H2-EB1k	G-DOMAIN G-BETA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202436-0)
C	TR 2B4	TR-ALPHA	Chimeric (chimeric)	TRAV4D-402, TRAJ5601, TRAC*01	V-DOMAIN V-ALPHA, C-DOMAIN C-ALPHA	TR	TR-ALPHA_BETA-2	IMGT (202436-0)
D	TR 2B4	TR-BETA-2	Chimeric (chimeric)	TRBV2601, TRBJ2-501, TRBC201, TRBC202	V-DOMAIN V-BETA, C-DOMAIN C-BETA-2	TR	TR-ALPHA_BETA-2	IMGT (202436-0)

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
B	PF00969	Class II histocompatibility antigen, beta domain (MHC_II_beta)	Class II histocompatibility antigen, beta domain	-	Domain
B	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
C	PF09291	Domain of unknown function (DUF1968) (DUF1968)	Domain of unknown function (DUF1968)	Members of this family are found in mammalian T-cell antigen receptor, and adopt an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function has not, as yet, been determined.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	H-2 class II histocompatibility antigen, E-K 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 peptide antigen assembly with MHC class II protein complex protein-containing complex organization 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 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 antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II cellular component assembly protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class II cellular process MHC protein complex assembly cellular component organization or biogenesis antigen processing and presentation of peptide 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 multicellular organismal process regulation of cellular process regulation of leukocyte 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 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 regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation	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 late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle
B	MHC class II E-beta-k	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 peptide antigen assembly with MHC class II protein complex protein-containing complex organization 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 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 antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II cellular component assembly protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class II cellular process MHC protein complex assembly cellular component organization or biogenesis antigen processing and presentation of peptide 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 multicellular organismal process regulation of cellular process regulation of leukocyte 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 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 regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation	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 late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle
C	T-cell receptor alpha chain C region	-	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 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 immune system process regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response adaptive immune response 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 biotic stimulus multicellular organismal process T cell activation cell activation alpha-beta T cell activation lymphocyte activation leukocyte activation	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex plasma membrane protein complex membrane protein complex alpha-beta T cell receptor complex receptor complex plasma membrane signaling receptor complex T cell receptor complex
D	2B4 beta chain	-	-	-
E [auth P]	MCC peptide	binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds cellular metabolic process ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, cytochrome c to oxygen respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds cellular metabolic process ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, cytochrome c to oxygen respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport mitochondrial electron transport, ubiquinol to cytochrome c	protein-containing complex membrane respirasome membrane protein complex cellular anatomical entity membrane-bounded organelle intracellular anatomical structure mitochondrial intermembrane space mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle envelope lumen intracellular organelle protein-containing complex membrane respirasome membrane protein complex cellular anatomical entity membrane-bounded organelle intracellular anatomical structure mitochondrial intermembrane space mitochondrion membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle envelope lumen intracellular organelle organelle envelope organelle lumen organelle mitochondrial envelope cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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
C	IPR052051	T cell receptor complex component	Family
C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C	IPR015370	T-cell receptor alpha chain, constant domain	Domain
E [auth P]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
E [auth P]	IPR009056	Cytochrome c-like domain	Domain
E [auth P]	IPR002327	Cytochrome c, class IA/ IB	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P01848	TCR-alpha-beta-positive T-cell deficiency B-cell chronic lymphocytic leukemia invasive ductal breast carcinoma malignant ependymoma Sjogren syndrome cutaneous lupus erythematosus large cell medulloblastoma medulloblastoma interstitial cystitis lung cancer osteosarcoma ulcerative colitis