2XNA | pdb_00002xna

Crystal structure of the complex between human T cell receptor and staphylococcal enterotoxin

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)
C	d2xnac1	All beta proteins	OB-fold	Bacterial enterotoxins	Superantigen toxins, N-terminal domain	Staphylococcal enterotoxin H, SEH	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C	d2xnac2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Superantigen toxins, C-terminal domain	Superantigen toxins, C-terminal domain	Staphylococcal enterotoxin H, SEH	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d2xnab1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2xnaa2	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)
A	d2xnaa1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Bacterial enterotoxins	8041895	3000434	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Superantigen toxins C-terminal domain-like	8034582	3000376	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054555	3000071	SCOP2B (2022-06-29)
A	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)
C	Stap_Strp_toxin	e2xnaC1	A: beta barrels	X: OB-fold	H: Bacterial enterotoxins (From Topology)	T: Bacterial enterotoxins	F: Stap_Strp_toxin	ECOD (1.6)
C	Stap_Strp_tox_C	e2xnaC2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Stap_Strp_tox_C	ECOD (1.6)
B	C1-set	e2xnaB2	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)
B	V-set_3	e2xnaB1	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	DUF1968	e2xnaA2	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_3	e2xnaA1	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)
C	3.10.20.120	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
C	2.40.50.110	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	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)

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
C	Superantigen enterotoxin type H (SEH)	Toxin	Staphylococcus aureus	entH*01	R-LIKE-DOMAIN SAG-DOMAIN	TOX	Protein	IMGT (202546-0)
B	TR	TR-BETA-2	Homo sapiens (human)	TRBV1901, TRBJ2-701, TRBC201, TRBC202	V-DOMAIN V-BETA, C-DOMAIN C-BETA-2	TR	TR-ALPHA_BETA-2	IMGT (202546-0)
A	TR	TR-ALPHA	Homo sapiens (human)	TRAV2701, TRAJ4201, TRAC*01	V-DOMAIN V-ALPHA, C-DOMAIN C-ALPHA	TR	TR-ALPHA_BETA-2	IMGT (202546-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	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
C	PF02876	Staphylococcal/Streptococcal toxin, beta-grasp domain (Stap_Strp_tox_C)	Staphylococcal/Streptococcal toxin, beta-grasp domain		Domain
B	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A	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
C	ENTEROTOXIN H	protein-containing complex binding protein binding binding signaling receptor binding T cell receptor binding MHC class II protein binding MHC protein binding cation binding ion binding metal ion binding small molecule binding toxin activity	-	cellular anatomical structure extracellular region
B	T CELL RECEPTOR BETA-1 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 multicellular organismal process T cell activation cell activation alpha-beta T cell activation lymphocyte activation leukocyte activation	cell periphery cellular anatomical structure plasma membrane membrane 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
A	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 cellular anatomical structure plasma membrane membrane 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR006123	Staphylococcal/Streptococcal toxin, beta-grasp domain	Domain
C	IPR006177	Staphylococcal/streptococcal toxin, bacterial	Family
C	IPR006126	Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site	Conserved Site
C	IPR016091	Superantigen toxin, C-terminal	Homologous Superfamily
C	IPR006173	Staphylococcal/Streptococcal toxin, OB-fold	Domain
C	IPR013307	Superantigen, staphylococcal/streptococcal toxin, bacterial	Family
C	IPR008992	Enterotoxin	Homologous Superfamily
B	IPR003597	Immunoglobulin C1-set	Domain
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR007110	Immunoglobulin-like domain	Domain
B	IPR050380	Immune Recognition and Response Modulators	Family
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR015370	T-cell receptor alpha chain, constant domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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

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.