2IJ0 | pdb_00002ij0

Structural basis of T cell specificity and activation by the bacterial superantigen toxic shock syndrome toxin-1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth E]	d2ij0e_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	T-cell antigen receptor	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth C]	d2ij0c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	T-cell antigen receptor	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ij0a1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Toxic shock syndrome toxin-1 (TSST-1)	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d2ij0a2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Superantigen toxins, C-terminal domain	Superantigen toxins, C-terminal domain	Toxic shock syndrome toxin-1 (TSST-1)	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C [auth B]	d2ij0b1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Toxic shock syndrome toxin-1 (TSST-1)	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C [auth B]	d2ij0b2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Superantigen toxins, C-terminal domain	Superantigen toxins, C-terminal domain	Toxic shock syndrome toxin-1 (TSST-1)	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth E]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054453	3000071	SCOP2B (2022-06-29)
D [auth C]	SCOP2 Family	V set domains-like	8054452	4007530	SCOP2 (2022-06-29)
D [auth C]	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8054453	3000071	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8042758	3000376	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacterial enterotoxins	8042756	3000434	SCOP2B (2022-06-29)
C [auth B]	SCOP2 Family	Superantigen toxins, N-terminal domain	8030377	4001839	SCOP2 (2022-06-29)
C [auth B]	SCOP2 Family	Superantigen toxins, C-terminal domain	8030379	4000990	SCOP2 (2022-06-29)
C [auth B]	SCOP2 Superfamily	Bacterial enterotoxins	8042756	3000434	SCOP2 (2022-06-29)
C [auth B]	SCOP2 Superfamily	Superantigen toxins C-terminal domain-like	8042758	3000376	SCOP2 (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 [auth E]	Copper-bind	e2ij0E1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (develop294)
D [auth C]	V-set	e2ij0C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (develop294)
A	Cpn10	e2ij0A1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Cpn10	ECOD (develop294)
A	S4	e2ij0A2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: S4	ECOD (develop294)
C [auth B]	Cpn10	e2ij0B1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Cpn10	ECOD (develop294)
C [auth B]	S4	e2ij0B2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: S4	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
A	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C [auth B]	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
C [auth B]	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth E], D [auth C]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth E], D [auth C]	penultimate affinity-matured variant of hVbeta 2.1, D10	-	immune system process	cell periphery cellular anatomical structure plasma membrane membrane
A, C [auth B]	Toxic shock syndrome toxin-1	toxin activity	-	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth E], D [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth E], D [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth E], D [auth C]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth E], D [auth C]	IPR007110	Immunoglobulin-like domain	Domain
B [auth E], D [auth C]	IPR050413	T cell receptor beta variable	Family
A, C [auth B]	IPR006123	Staphylococcal/Streptococcal toxin, beta-grasp domain	Domain
A, C [auth B]	IPR006126	Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site	Conserved Site
A, C [auth B]	IPR016091	Superantigen toxin, C-terminal	Homologous Superfamily
A, C [auth B]	IPR013307	Superantigen, staphylococcal/streptococcal toxin, bacterial	Family
A, C [auth B]	IPR008992	Enterotoxin	Homologous Superfamily

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.