2AQ1 | pdb_00002aq1

Crystal structure of T-cell receptor V beta domain variant complexed with superantigen SEC3 mutant

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	d2aq1b1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin C3, SEC3	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d2aq1b2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Superantigen toxins, C-terminal domain	Superantigen toxins, C-terminal domain	Staphylococcal enterotoxin C3, SEC3	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
D	d2aq1d1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin C3, SEC3	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
D	d2aq1d2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Superantigen toxins, C-terminal domain	Superantigen toxins, C-terminal domain	Staphylococcal enterotoxin C3, SEC3	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
F	d2aq1f1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin C3, SEC3	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
F	d2aq1f2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Superantigen toxins, C-terminal domain	Superantigen toxins, C-terminal domain	Staphylococcal enterotoxin C3, SEC3	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
H	d2aq1h1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin C3, SEC3	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
H	d2aq1h2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Superantigen toxins, C-terminal domain	Superantigen toxins, C-terminal domain	Staphylococcal enterotoxin C3, SEC3	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
G	d2aq1g_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d2aq1e_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d2aq1c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2aq1a_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	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)
B	SCOP2B Superfamily	Bacterial enterotoxins	8042829	3000434	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8042830	3000376	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8042830	3000376	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bacterial enterotoxins	8042829	3000434	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Bacterial enterotoxins	8042829	3000434	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8042830	3000376	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8042830	3000376	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Bacterial enterotoxins	8042829	3000434	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055394	3000071	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055394	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055394	3000071	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055394	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)
B	Stap_Strp_toxin	e2aq1B1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Stap_Strp_toxin	ECOD (1.6)
B	Stap_Strp_tox_C	e2aq1B2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Stap_Strp_tox_C	ECOD (1.6)
D	Stap_Strp_toxin	e2aq1D1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Stap_Strp_toxin	ECOD (1.6)
D	Stap_Strp_tox_C	e2aq1D2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Stap_Strp_tox_C	ECOD (1.6)
F	Stap_Strp_toxin	e2aq1F1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Stap_Strp_toxin	ECOD (1.6)
F	Stap_Strp_tox_C	e2aq1F2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Stap_Strp_tox_C	ECOD (1.6)
H	Stap_Strp_toxin	e2aq1H1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Stap_Strp_toxin	ECOD (1.6)
H	Stap_Strp_tox_C	e2aq1H2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Stap_Strp_tox_C	ECOD (1.6)
G	V-set_3	e2aq1G1	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)
E	V-set_3	e2aq1E1	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	V-set_3	e2aq1C1	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)
A	V-set_3	e2aq1A1	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)
B	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
B	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
D	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
F	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
F	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
H	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
H	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
G	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)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF01123	Staphylococcal/Streptococcal toxin, OB-fold domain (Stap_Strp_toxin)	Staphylococcal/Streptococcal toxin, OB-fold domain	This entry represents an OB-fold domain found in enterotoxins.	Domain
B, D, F, H	PF02876	Staphylococcal/Streptococcal toxin, beta-grasp domain (Stap_Strp_tox_C)	Staphylococcal/Streptococcal toxin, beta-grasp domain		Domain
A, C, E, G	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, D, F, H	Enterotoxin type C-3	cation binding ion binding binding metal ion binding small molecule binding toxin activity	-	cellular anatomical structure extracellular region
A, C, E, G	T-cell receptor beta chain V	-	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex T cell receptor complex receptor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR006123	Staphylococcal/Streptococcal toxin, beta-grasp domain	Domain
B, D, F, H	IPR006177	Staphylococcal/streptococcal toxin, bacterial	Family
B, D, F, H	IPR006126	Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site	Conserved Site
B, D, F, H	IPR016091	Superantigen toxin, C-terminal	Homologous Superfamily
B, D, F, H	IPR006173	Staphylococcal/Streptococcal toxin, OB-fold	Domain
B, D, F, H	IPR013307	Superantigen, staphylococcal/streptococcal toxin, bacterial	Family
B, D, F, H	IPR008992	Enterotoxin	Homologous Superfamily
A, C, E, G	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C, E, G	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR013106	Immunoglobulin V-set domain	Domain
A, C, E, G	IPR003599	Immunoglobulin domain subtype	Domain
A, C, E, G	IPR007110	Immunoglobulin-like domain	Domain
A, C, E, G	IPR050413	T cell receptor beta variable	Family

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.