3L9R | pdb_00003l9r

Crystal structure of bovine CD1b3 with endogenously bound ligands

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3l9ra2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d3l9ra1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d3l9ra3	Artifacts	Tags	Tags	Tags	C-terminal Tags	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C	d3l9rc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C	d3l9rc1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C	d3l9rc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
E	d3l9re2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
E	d3l9re1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
E	d3l9re3	Artifacts	Tags	Tags	Tags	C-terminal Tags	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
G	d3l9rg2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
G	d3l9rg1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
G	d3l9rg3	Artifacts	Tags	Tags	Tags	C-terminal Tags	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d3l9rb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	beta2-microglobulin	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D	d3l9rd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	beta2-microglobulin	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
F	d3l9rf_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	beta2-microglobulin	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
H	d3l9rh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	beta2-microglobulin	bovine,cow,domestic cattle,domestic cow (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054563	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054563	3000071	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054563	3000071	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054563	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)
A		e3l9rA1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Cu,Zn superoxide dismutase-like	T: ManC_GMP_beta-helix	F:	ECOD (20:10:01)
C		e3l9rC1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
E		e3l9rE1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
G		e3l9rG1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
B		e3l9rB1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
D		e3l9rD1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
F		e3l9rF1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)
H		e3l9rH1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T: Cytochrome_CBB3	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	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, C, E, G	CD1B3	I-ALPHA-LIKE	Bos taurus (bovine)	CD1B3*01	G-DOMAIN G-ALPHA1-LIKE, G-DOMAIN G-ALPHA2-LIKE, C-LIKE-DOMAIN C-LIKE	RPI-MH1Like	MH1LIKE-ALPHA-LIKE_B2M	IMGT (202609-0)
B, D, F, H	CD1B3	B2M	Bos taurus (bovine)	B2M*01	C-LIKE-DOMAIN C-LIKE	RPI-MH1Like	MH1LIKE-ALPHA-LIKE_B2M	IMGT (202609-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	CD1b3	binding lipid binding lipopeptide binding antigen binding exogenous lipid antigen binding lipid antigen binding endogenous lipid antigen binding	response to stimulus immune response immune system process adaptive immune response antigen processing and presentation antigen processing and presentation of lipid antigen via MHC class Ib antigen processing and presentation via MHC class Ib antigen processing and presentation of endogenous antigen antigen processing and presentation, endogenous lipid antigen via MHC class Ib antigen processing and presentation of exogenous antigen antigen processing and presentation, exogenous lipid antigen via MHC class Ib adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process response to stimulus immune response immune system process adaptive immune response antigen processing and presentation antigen processing and presentation of lipid antigen via MHC class Ib antigen processing and presentation via MHC class Ib antigen processing and presentation of endogenous antigen antigen processing and presentation, endogenous lipid antigen via MHC class Ib antigen processing and presentation of exogenous antigen antigen processing and presentation, exogenous lipid antigen via MHC class Ib adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of biological process 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 immune response positive regulation of leukocyte mediated cytotoxicity leukocyte mediated immunity regulation of immune system process positive regulation of immune effector process positive regulation of adaptive immune response positive regulation of immune system process positive regulation of cellular process regulation of T cell mediated immunity T cell mediated cytotoxicity regulation of biological process positive regulation of T cell mediated cytotoxicity regulation of adaptive immune response biological regulation regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity regulation of T cell mediated cytotoxicity regulation of lymphocyte mediated immunity regulation of response to stimulus positive regulation of T cell mediated immunity regulation of immune response regulation of cell killing cellular process positive regulation of cell killing cell killing	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane vacuolar membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane vacuolar membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane cytoplasm organelle membrane lysosome endosome membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle extracellular region extracellular space
B, D, F, H	Beta-2-microglobulin	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process peptide antigen assembly with MHC class II protein complex protein-containing complex organization regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II cellular component assembly protein-containing complex assembly antigen processing and presentation of peptide antigen via MHC class II cellular process MHC protein complex assembly cellular component organization or biogenesis antigen processing and presentation of peptide antigen response to metal ion response to chemical antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of exogenous antigen antigen processing and presentation of peptide antigen via MHC class I multicellular organismal process regulation of cellular process regulation of leukocyte activation 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 cell-cell adhesion positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation	vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm vacuolar membrane membrane-bounded organelle intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle lysosomal membrane cytoplasm organelle membrane lysosome extracellular region MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex MHC class I protein complex endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR050208	Antigen-presenting and immune regulatory MHC class I-related	Family
A, C, E, G	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
A, C, E, G	IPR003597	Immunoglobulin C1-set	Domain
A, C, E, G	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C, E, G	IPR011161	MHC class I-like antigen recognition-like	Domain
A, C, E, G	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A, C, E, G	IPR007110	Immunoglobulin-like domain	Domain
B, D, F, H	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, D, F, H	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B, D, F, H	IPR003597	Immunoglobulin C1-set	Domain
B, D, F, H	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D, F, H	IPR015707	Beta-2-Microglobulin	Family
B, D, F, H	IPR007110	Immunoglobulin-like domain	Domain
B, D, F, H	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.