7JOO

Crystal structure of ICOS in complex with antibody STIM003 and anti-kappa VHH domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab 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)
B [auth H]	d7jooh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d7jool1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d7jool2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth C]	F_UNCLASSIFIED	e7jooC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: F_UNCLASSIFIED	ECOD (1.6)
A [auth K]	V-set_10	e7jooK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
B [auth H]	C1-set_1	e7jooH1	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 [auth H]	V-set_12	e7jooH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
C [auth L]	C1-set_4	e7jooL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
C [auth L]	V-set	e7jooL2	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 (1.6)

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
D [auth C]	ICOS 3-232 (Pr19-248)(O75144)	1C-LIKE	Homo sapiens (human)	ICOS	V-LIKE-DOMAIN V-LIKE	-	Protein	IMGT (202442-0)
B [auth H]	Fab STIM003, anti-ICOS-L	VH-CH1	Homo sapiens (human)	IGHV3-2004, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG107, IGHG109, IGHG110, IGHG111, IGHG112, IGHG113, IGHG1*14	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)
C [auth L]	Fab STIM003, anti-ICOS-L	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ301, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202442-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV3	-	inducible t-cell costimulator	SAbDab (2024-10-25)
C [auth L]	Light Chain	IGKV3	Kappa	inducible t-cell costimulator	SAbDab (2024-10-25)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B [auth H]	Alomfilimab	ICOS/CD278	Therapeutic SAbDab (2024-10-25)
C [auth L]	Alomfilimab	ICOS/CD278	Therapeutic SAbDab (2024-10-25)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth C]	PF15910	ICOS V-set domain (V-set_2)	ICOS V-set domain	This family contains divergent V-set ig domains found in the ICOS protein.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth C]	Inducible T-cell costimulator	-	multicellular organismal process regulation of cellular process regulation of leukocyte 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 multicellular organismal process regulation of cellular process regulation of leukocyte 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 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 immune system process lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process cellular process T cell costimulation regulation of lymphocyte activation immune system development developmental process multicellular organism development T cell tolerance induction anatomical structure development tolerance induction system development response to stimulus immune response	cell periphery plasma membrane membrane cellular anatomical entity extracellular region
A [auth K]	anti-kappa VHH	-	-	-
B [auth H]	STIM003 Fab Heavy chain	-	-	-
C [auth L]	STIM003 Fab Light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth C]	IPR039943	Inducible T-cell costimulator	Family
D [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth C]	IPR013106	Immunoglobulin V-set domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth C]	Pharos: Q9Y6W8	common variable immunodeficiency adult T-cell leukemia/lymphoma immunodeficiency, common variable, 1 alopecia areata psoriasis skin basal cell carcinoma Acquired Hypogammaglobulinemia agammaglobulinemia celiac disease Graves disease interstitial cystitis myasthenia gravis rheumatoid arthritis vitiligo acute T cell leukemia common variable immunodeficiency adult T-cell leukemia/lymphoma immunodeficiency, common variable, 1 alopecia areata psoriasis skin basal cell carcinoma Acquired Hypogammaglobulinemia agammaglobulinemia celiac disease Graves disease interstitial cystitis myasthenia gravis rheumatoid arthritis vitiligo acute T cell leukemia Hashimoto thyroiditis immunodeficiency, common variable, 2 lung cancer osteosarcoma Sjogren syndrome B cell deficiency cutaneous lupus erythematosus hypothyroidism lung carcinoma

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.