3C6L | pdb_00003c6l

Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR 2W20

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	d3c6la1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain lambda variable domain, VL-lambda	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3c6la2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	T-cell antigen receptor	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3c6le1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain lambda variable domain, VL-lambda	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3c6le2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	T-cell antigen receptor	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3c6lc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC alpha chain, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3c6lc2	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	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d3c6lg1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC alpha chain, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d3c6lg2	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	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3c6ld1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC beta chain, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ], house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3c6ld2	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	house mouse (Mus musculus ) [TaxId: 10090 ], house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H	d3c6lh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC beta chain, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ], house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H	d3c6lh2	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	house mouse (Mus musculus ) [TaxId: 10090 ], house 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)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054687	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MHC antigen-recognition domain	8043807	3000521	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	MHC antigen-recognition domain	8043807	3000521	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054687	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MHC antigen-recognition domain	8043808	3000521	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054723	3000071	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	MHC antigen-recognition domain	8043808	3000521	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054723	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	DUF1968	e3c6lA2	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)
A	V-set_4	e3c6lA1	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)
E	DUF1968	e3c6lE2	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)
E	V-set_4	e3c6lE1	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)
B	C1-set_1	e3c6lB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B	V-set_3	e3c6lB1	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)
F	C1-set_1	e3c6lF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F	V-set_3	e3c6lF1	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)
C	C1-set_2	e3c6lC1	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)
C	MHC_II_alpha	e3c6lC2	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)
G	C1-set_2	e3c6lG1	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)
G	MHC_II_alpha	e3c6lG2	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	e3c6lD1	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_beta	e3c6lD2	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)
H	C1-set_2	e3c6lH1	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)
H	MHC_II_beta	e3c6lH2	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	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
G	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)
H	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
H	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, E	TR 2W20	TR-ALPHA	Mus musculus (house mouse)	TRAV14-202, TRAJ3101, TRAJ3102, TRAC01	V-DOMAIN V-ALPHA, C-DOMAIN C-ALPHA	TR	TR-ALPHA_BETA-1	IMGT (202529-0)
B, F	TR 2W20	TR-BETA-1	Mus musculus (house mouse)	TRBV13-201, TRBJ2-701, TRBJ2-702, TRBC101, TRBC201, TRBC203	V-DOMAIN V-BETA, C-DOMAIN C-BETA-1	TR	TR-ALPHA_BETA-1	IMGT (202529-0)
C, G	MH2-AA_MH2-EBu, IAb-3K 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 (202529-0)
D, H	MH2-AA_MH2-EBu, IAb-3K peptide fused to N-terminus of G-BETA	II-BETA	Mus musculus (house mouse)	H2-AB1*01	G-DOMAIN G-BETA	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202529-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E	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
B, F	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
C, G	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
C, G	PF00993	Class II histocompatibility antigen, alpha domain (MHC_II_alpha)	Class II histocompatibility antigen, alpha domain		Domain
D, H	PF00969	Class II histocompatibility antigen, beta domain (MHC_II_beta)	Class II histocompatibility antigen, beta domain		Domain
D, H	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, E	TCR 2W20 alpha chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex T cell receptor complex receptor complex
B, F	TCR 2W20 beta chain	-	-	protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex alpha-beta T cell receptor complex receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex T cell receptor complex
C, G	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 antigen processing and presentation of exogenous peptide antigen via MHC class II 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
D, H	3K peptide, Linker,and H-2 class II histocompatibility antigen (A beta chain)	protein antigen binding protein binding binding antigen binding peptide antigen binding peptide binding toxic substance binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	response to stimulus immune response immune system process 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 response to stimulus immune response immune system process 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 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 cellular response to type II interferon response to biotic stimulus response to peptide response to chemical defense response to other organism response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus regulation of antigen processing and presentation positive regulation of antigen processing and presentation	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 anatomical structure 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 anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome cytoplasm multivesicular body vesicle early endosome Golgi apparatus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, E	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, E	IPR015370	T-cell receptor alpha chain, constant domain	Domain
B, F	IPR003597	Immunoglobulin C1-set	Domain
B, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, F	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, F	IPR007110	Immunoglobulin-like domain	Domain
B, F	IPR050380	Immune Recognition and Response Modulators	Family
C, G	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, G	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
C, G	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
C, G	IPR003597	Immunoglobulin C1-set	Domain
C, G	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, G	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
C, G	IPR007110	Immunoglobulin-like domain	Domain
C, G	IPR001003	MHC class II, alpha chain, N-terminal	Domain
C, G	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D, H	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D, H	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
D, H	IPR003597	Immunoglobulin C1-set	Domain
D, H	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
D, H	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D, H	IPR000353	MHC class II, beta chain, N-terminal	Domain
D, H	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
D, H	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D, H	IPR007110	Immunoglobulin-like domain	Domain