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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
B [auth E]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054453	3000071	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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth C]	V-set_3	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_3	ECOD (1.6)
B [auth E]	V-set_3	e2ij0E1	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 [auth B]	UNK_F_TYPE	e2ij0B1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: UNK_F_TYPE	ECOD (1.6)
C [auth B]	Stap_Strp_tox_C	e2ij0B2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Stap_Strp_tox_C	ECOD (1.6)
A	UNK_F_TYPE	e2ij0A1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: UNK_F_TYPE	ECOD (1.6)
A	Stap_Strp_tox_C	e2ij0A2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Stap_Strp_tox_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.2.0)
B [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.2.0)
C [auth B]	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.2.0)
C [auth B]	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.2.0)
A	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.2.0)
A	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.2.0)

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
A, C [auth B]	PF02876	Staphylococcal/Streptococcal toxin, beta-grasp domain (Stap_Strp_tox_C)	Staphylococcal/Streptococcal toxin, beta-grasp domain		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.