4ADQ | pdb_00004adq

CRYSTAL STRUCTURE OF THE MOUSE COLONY-STIMULATING FACTOR 1 (MCSF-1) CYTOKINE IN COMPLEX WITH THE VIRAL RECEPTOR BARF1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	4-helical cytokines	8074034	3001717	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	4-helical cytokines	8074034	3001717	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	4-helical cytokines	8074034	3001717	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	4-helical cytokines	8074034	3001717	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)
E	ABC_tran	e4adqE1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
F	ABC_tran	e4adqF1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
G	ABC_tran	e4adqG1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
H	ABC_tran	e4adqH1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
B	RRM_1	e4adqB1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
C	RRM_1	e4adqC1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
D	RRM_1	e4adqD1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
A	RRM_1	e4adqA1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)

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, B, C, D	Secreted protein BARF1	1V-1C-LIKE	Homo sapiens (human)	BARF1	V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE	RPI	1V-1C-LIKE	IMGT (202610-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F, G, H	PF05337	Macrophage colony stimulating factor-1 (CSF-1) (CSF-1)	Macrophage colony stimulating factor-1 (CSF-1)	Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mono ...	Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility [1] and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption [2]. Structurally these are short-chain 4-helical cytokines.	Domain
A, B, C, D	PF22305	BARF1 second Ig-like domain (BARF1_ig2)	BARF1 second Ig-like domain	This entry represents the second Immunoglobulin-like domain present in the BARF1 protein from Epstein-Barr virus [1,2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	MACROPHAGE COLONY-STIMULATING FACTOR 1	molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding cytokine receptor binding macrophage colony-stimulating factor receptor binding identical protein binding protein homodimerization activity protein dimerization activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity protein binding binding signaling receptor binding cytokine receptor binding macrophage colony-stimulating factor receptor binding identical protein binding protein homodimerization activity protein dimerization activity cytokine activity	regulation of biological process regulation of cellular process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process metabolic process cellular process positive regulation of macromolecule metabolic process protein metabolic process regulation of biological process regulation of cellular process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process metabolic process cellular process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus regulation of macrophage colony-stimulating factor signaling pathway signaling response to cytokine regulation of signal transduction regulation of response to macrophage colony-stimulating factor positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of response to stimulus regulation of cellular response to macrophage colony-stimulating factor stimulus cellular response to cytokine stimulus signal transduction positive regulation of macrophage colony-stimulating factor signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of cytokine-mediated signaling pathway macrophage colony-stimulating factor signaling pathway response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus response to peptide regulation of response to cytokine stimulus regulation of response to stimulus response to chemical regulation of cell communication positive regulation of cytokine-mediated signaling pathway positive regulation of signaling developmental process multicellular organismal process regulation of animal organ morphogenesis regulation of developmental process regulation of odontogenesis of dentin-containing tooth regulation of odontogenesis odontogenesis of dentin-containing tooth odontogenesis animal organ development positive regulation of odontogenesis positive regulation of developmental process anatomical structure morphogenesis positive regulation of odontogenesis of dentin-containing tooth positive regulation of animal organ morphogenesis anatomical structure development positive regulation of multicellular organismal process animal organ morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells within a tissue anatomical structure homeostasis tissue homeostasis homeostasis of number of cells positive regulation of locomotion regulation of cell motility cellular developmental process regulation of microglial cell migration glial cell migration macrophage migration regulation of glial cell migration positive regulation of cell migration neurogenesis multicellular organism development regulation of macrophage migration gliogenesis cell differentiation positive regulation of cell motility regulation of cell migration myeloid leukocyte migration positive regulation of mononuclear cell migration positive regulation of microglial cell migration cell migration regulation of immune system process regulation of mononuclear cell migration cell motility positive regulation of immune system process locomotion system development positive regulation of macrophage migration regulation of leukocyte migration microglial cell migration positive regulation of leukocyte migration nervous system development leukocyte migration positive regulation of glial cell migration immune system process regulation of locomotion mononuclear cell migration regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion cell adhesion cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion regulation of biosynthetic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process response to stress response to ischemia biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism innate immune response response to external biotic stimulus connective tissue development adipose tissue development mammary gland development mammary gland fat development gland development tissue development ossification regulation of ossification macrophage derived foam cell differentiation regulation of cell differentiation foam cell differentiation positive regulation of cell differentiation regulation of macrophage derived foam cell differentiation positive regulation of macrophage derived foam cell differentiation positive regulation of chemotaxis taxis chemotaxis regulation of leukocyte chemotaxis positive regulation of leukocyte chemotaxis granulocyte migration regulation of response to external stimulus macrophage chemotaxis regulation of granulocyte chemotaxis positive regulation of response to external stimulus cell chemotaxis regulation of macrophage chemotaxis regulation of chemotaxis cellular response to chemical stimulus granulocyte chemotaxis positive regulation of macrophage chemotaxis leukocyte chemotaxis cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation developmental growth mammary gland morphogenesis tube morphogenesis gland morphogenesis mammary duct terminal end bud growth epithelial tube morphogenesis epithelium development tube development growth morphogenesis of an epithelium developmental growth involved in morphogenesis mammary gland duct morphogenesis tissue morphogenesis mammary gland epithelium development regulation of leukocyte proliferation leukocyte proliferation macrophage proliferation positive regulation of leukocyte proliferation positive regulation of macrophage proliferation regulation of macrophage proliferation myeloid leukocyte differentiation hemopoiesis macrophage differentiation cell development mononuclear cell differentiation myeloid cell differentiation leukocyte differentiation regulation of leukocyte differentiation positive regulation of monocyte differentiation regulation of cell development positive regulation of hemopoiesis monocyte differentiation regulation of multicellular organismal development regulation of monocyte differentiation regulation of myeloid cell differentiation positive regulation of cell development regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation mononuclear cell proliferation positive regulation of mononuclear cell proliferation regulation of mononuclear cell proliferation cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway regulation of multicellular organism growth regulation of growth regulation of developmental growth positive regulation of multicellular organism growth multicellular organism growth positive regulation of growth positive regulation of developmental growth microglial cell proliferation glial cell proliferation osteoclast proliferation regulation of macrophage differentiation positive regulation of macrophage differentiation branching involved in mammary gland duct morphogenesis branching morphogenesis of an epithelial tube morphogenesis of a branching structure morphogenesis of a branching epithelium osteoclast differentiation reproductive process developmental process involved in reproduction inflammatory response small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction intracellular signal transduction regulation of intracellular signal transduction regulation of Ras protein signal transduction intracellular signaling cassette positive regulation of Ras protein signal transduction Ras protein signal transduction positive regulation of intracellular signal transduction positive regulation of small GTPase mediated signal transduction positive regulation of osteoclast differentiation regulation of osteoclast differentiation	cell periphery cellular anatomical structure plasma membrane membrane CSF1-CSF1R complex protein-containing complex extracellular region intracellular anatomical structure perinuclear region of cytoplasm cytoplasm extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen cell periphery cellular anatomical structure plasma membrane membrane CSF1-CSF1R complex protein-containing complex extracellular region intracellular anatomical structure perinuclear region of cytoplasm cytoplasm extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen
A, B, C, D	SECRETED PROTEIN BARF1	identical protein binding protein binding binding	-	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR008001	Macrophage colony stimulating factor-1	Family
E, F, G, H	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily
A, B, C, D	IPR054777	BARF1, second Ig-like domain	Domain
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR007110	Immunoglobulin-like domain	Domain

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.