1YJD

Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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)
A [auth L]	d1yjdl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d1yjdl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1yjdh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1yjdh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d1yjdc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD28	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	SCOP2 Family	V set domains-like	8054534	4007530	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8054535	3000071	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)
A [auth L]	C1-set_4	e1yjdL2	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)
A [auth L]	V-set	e1yjdL1	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)
B [auth H]	V-set_8	e1yjdH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth H]	C1-set_1	e1yjdH1	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)
C	V-set_5	e1yjdC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	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)

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
A [auth L]	5.11A1	L-KAPPA	Mus musculus (house mouse)	IGKV10-9401, IGKV10-9402, IGKV10-9403, IGKV10-9601, IGKV10-9602, IGKV10-9404, IGKV10-9406, IGKV10-9405, IGKV10-9408, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202450-0)
B [auth H]	5.11A1	VH-CH1	Mus musculus (house mouse)	IGHV1S1201, IGHJ101, IGHJ102, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202450-0)
C	CD28	1V-LIKE	Homo sapiens (human)	CD28*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202450-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV10	Kappa	t-cell-specific surface glycoprotein cd28	SAbDab (2024-12-20)
B [auth H]	Heavy Chain	IGHV1	-	t-cell-specific surface glycoprotein cd28	SAbDab (2024-12-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
A [auth L]	Fab fragment of 5.11A1 antibody light chain	-	-	-
B [auth H]	Fab fragment of 5.11A1 antibody heavy chain	-	-	-
C	T-cell-specific surface glycoprotein CD28	molecular transducer activity coreceptor activity signaling receptor activity protein binding binding kinase binding enzyme binding protein kinase binding identical protein binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains response to stimulus regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response positive regulation of macromolecule biosynthetic process regulation of primary metabolic process multicellular organism development positive regulation of immune response regulation of immune system process positive regulation of macromolecule metabolic process system development positive regulation of DNA recombination positive regulation of immunoglobulin mediated immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains response to stimulus regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response positive regulation of macromolecule biosynthetic process regulation of primary metabolic process multicellular organism development positive regulation of immune response regulation of immune system process positive regulation of macromolecule metabolic process system development positive regulation of DNA recombination positive regulation of immunoglobulin mediated immune response immune response DNA recombination primary metabolic process DNA metabolic process immune effector process regulation of gene expression biosynthetic process positive regulation of DNA metabolic process regulation of response to stimulus B cell mediated immunity positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process metabolic process regulation of DNA metabolic process immunoglobulin production regulation of developmental process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains somatic cell DNA recombination somatic diversification of immunoglobulins involved in immune response positive regulation of lymphocyte activation somatic recombination of immunoglobulin gene segments positive regulation of biosynthetic process regulation of immunoglobulin mediated immune response leukocyte activation involved in immune response regulation of B cell activation positive regulation of isotype switching positive regulation of immune effector process positive regulation of cellular process production of molecular mediator of immune response positive regulation of immunoglobulin production regulation of isotype switching cell activation regulation of macromolecule metabolic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression immune system process somatic diversification of immune receptors via germline recombination within a single locus cellular process regulation of lymphocyte activation lymphocyte mediated immunity regulation of immune effector process multicellular organismal process regulation of DNA recombination positive regulation of leukocyte mediated immunity regulation of cellular process cell activation involved in immune response nucleobase-containing compound metabolic process positive regulation of developmental process positive regulation of cell activation positive regulation of metabolic process anatomical structure development positive regulation of leukocyte activation leukocyte mediated immunity somatic diversification of immune receptors regulation of nucleobase-containing compound metabolic process positive regulation of adaptive immune response positive regulation of immune system process somatic recombination of immunoglobulin genes involved in immune response developmental process regulation of biological process positive regulation of nucleobase-containing compound metabolic process regulation of adaptive immune response regulation of B cell mediated immunity somatic diversification of immunoglobulins regulation of leukocyte mediated immunity regulation of immune response positive regulation of multicellular organismal process regulation of production of molecular mediator of immune response macromolecule metabolic process regulation of metabolic process isotype switching immune system development immunoglobulin production involved in immunoglobulin-mediated immune response positive regulation of lymphocyte mediated immunity positive regulation of biological process lymphocyte activation positive regulation of B cell mediated immunity leukocyte activation positive regulation of response to stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of isotype switching to IgG isotypes regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of biosynthetic process B cell activation biological regulation gene expression adaptive immune response immunoglobulin mediated immune response positive regulation of B cell activation regulation of isotype switching to IgG isotypes regulation of lymphocyte mediated immunity regulation of immunoglobulin production isotype switching to IgG isotypes thymic T cell selection cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation T cell differentiation in thymus T cell activation cell differentiation negative thymic T cell selection T cell differentiation negative T cell selection T cell selection leukocyte differentiation cellular response to stimulus immune response-regulating cell surface receptor signaling pathway signaling cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway antigen receptor-mediated signaling pathway activation of immune response humoral immune response intracellular signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death RNA metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction regulation of signal transduction regulation of intracellular signal transduction regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of cell communication positive regulation of signaling positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of mitotic nuclear division positive regulation of mitotic nuclear division mitotic cell cycle cellular component organization regulation of mitotic cell cycle positive regulation of cell cycle process cellular component organization or biogenesis cell cycle regulation of cell cycle cell cycle process mitotic nuclear division regulation of cell cycle process organelle fission positive regulation of nuclear division regulation of organelle organization positive regulation of cell cycle organelle organization nuclear division mitotic cell cycle process regulation of nuclear division regulatory T cell differentiation positive regulation of protein metabolic process positive regulation of translation post-transcriptional regulation of gene expression protein metabolic process regulation of protein metabolic process translation regulation of translation regulation of leukocyte differentiation regulation of cell differentiation regulation of cell development regulation of T cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development regulation of regulatory T cell differentiation regulation of T cell activation regulation of hemopoiesis positive regulation of viral genome replication positive regulation of viral process viral life cycle regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication positive regulation of cell population proliferation regulation of alpha-beta T cell activation positive regulation of alpha-beta T cell proliferation positive regulation of CD4-positive, alpha-beta T cell proliferation alpha-beta T cell proliferation lymphocyte proliferation alpha-beta T cell activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of alpha-beta T cell activation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion leukocyte proliferation leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of alpha-beta T cell proliferation positive regulation of CD4-positive, alpha-beta T cell activation cell adhesion cell-cell adhesion CD4-positive, alpha-beta T cell activation positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation CD4-positive, alpha-beta T cell proliferation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell proliferation regulation of CD4-positive, alpha-beta T cell activation regulation of mononuclear cell proliferation regulation of cytokine production cytokine production regulation of interleukin-2 production interleukin-2 production positive regulation of interleukin-2 production positive regulation of cytokine production interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production apoptotic signaling pathway lymphocyte costimulation T cell costimulation regulation of defense response regulation of response to external stimulus inflammatory response to antigenic stimulus positive regulation of response to external stimulus positive regulation of inflammatory response response to stress regulation of response to stress defense response regulation of inflammatory response to antigenic stimulus response to external stimulus regulation of inflammatory response positive regulation of inflammatory response to antigenic stimulus positive regulation of defense response inflammatory response negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production positive regulation of DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm cytosol immunological synapse protein-containing complex protein complex involved in cell adhesion

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C	IPR013106	Immunoglobulin V-set domain	Domain
C	IPR040216	Cytotoxic T-lymphocyte protein 4/CD28	Family
C	IPR008093	T cell antigen CD28	Family
C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P10747	rheumatoid arthritis autoimmune disease adult T-cell leukemia/lymphoma HIV infectious disease mature T-cell and NK-cell non-Hodgkin lymphoma mycosis fungoides primary cutaneous T-cell non-Hodgkin lymphoma chronic beryllium disease Sezary syndrome Chloracne lymphatic system disease acute T cell leukemia sarcoidosis Sjogren syndrome cancer rheumatoid arthritis autoimmune disease adult T-cell leukemia/lymphoma HIV infectious disease mature T-cell and NK-cell non-Hodgkin lymphoma mycosis fungoides primary cutaneous T-cell non-Hodgkin lymphoma chronic beryllium disease Sezary syndrome Chloracne lymphatic system disease acute T cell leukemia sarcoidosis Sjogren syndrome cancer granulomatous slack skin disease interstitial cystitis osteosarcoma primary biliary cholangitis psoriasis sclerosing cholangitis celiac disease cutaneous lupus erythematosus Hashimoto thyroiditis lung cancer ovarian cancer primary cutaneous T-cell lymphoma arthritic joint disease demyelinating disease hematologic disease inflammatory bowel disease

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.