3EJJ

Structure of M-CSF bound to the first three domains of FMS

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d3ejja1	All alpha proteins	4-helical cytokines	4-helical cytokines	Short-chain cytokines	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3ejja2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3ejjb_	All alpha proteins	4-helical cytokines	4-helical cytokines	Short-chain cytokines	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Short-chain cytokines	8074033	4000852	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	4-helical cytokines	8074034	3001717	SCOP2 (2022-06-29)
B	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)
A	CSF-1	e3ejjA1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: CSF-1	ECOD (1.6)
B	CSF-1	e3ejjB1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: CSF-1	ECOD (1.6)
C [auth X]	I-set_4	e3ejjX3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_4	ECOD (1.6)
C [auth X]	IG_like	e3ejjX2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: IG_like	ECOD (1.6)
C [auth X]	I-set	e3ejjX1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
B	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
C [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
C [auth X]	PF00047	Immunoglobulin domain (ig)	Immunoglobulin domain	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prote ...	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Colony stimulating factor-1	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity identical protein binding cytokine receptor binding macrophage colony-stimulating factor receptor binding protein homodimerization activity protein dimerization activity protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity identical protein binding cytokine receptor binding macrophage colony-stimulating factor receptor binding protein homodimerization activity protein dimerization activity cytokine activity	multicellular organismal process 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 regulation of cellular process cellular developmental process regulation of microglial cell migration glial cell migration positive regulation of biological process multicellular organismal process 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 regulation of cellular process cellular developmental process regulation of microglial cell migration glial cell migration positive regulation of biological process 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 anatomical structure development 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 positive regulation of cellular process system development developmental process regulation of biological process positive regulation of macrophage migration regulation of leukocyte migration biological regulation 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 cellular process 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 regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process response to stimulus 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 animal organ development tissue development cellular response to stimulus positive regulation of chemotaxis taxis chemotaxis regulation of leukocyte chemotaxis positive regulation of leukocyte chemotaxis granulocyte migration regulation of response to stimulus response to chemical regulation of response to external stimulus macrophage chemotaxis positive regulation of response to stimulus 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 myeloid leukocyte differentiation regulation of leukocyte differentiation positive regulation of monocyte differentiation regulation of developmental process cell development regulation of cell differentiation mononuclear cell differentiation regulation of cell development positive regulation of developmental process positive regulation of cell differentiation positive regulation of hemopoiesis regulation of multicellular organismal process monocyte differentiation regulation of multicellular organismal development regulation of monocyte differentiation hemopoiesis regulation of myeloid cell differentiation positive regulation of cell development regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation myeloid cell differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of multicellular organismal process positive regulation of leukocyte differentiation leukocyte differentiation regulation of leukocyte proliferation cell population proliferation positive regulation of cell population proliferation leukocyte proliferation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation positive regulation of mononuclear cell proliferation regulation of mononuclear cell proliferation osteoclast proliferation regulation of macrophage differentiation macrophage differentiation positive regulation of macrophage differentiation branching involved in mammary gland duct morphogenesis mammary gland morphogenesis branching morphogenesis of an epithelial tube tube morphogenesis gland morphogenesis animal organ morphogenesis epithelial tube morphogenesis epithelium development tube development morphogenesis of an epithelium mammary gland duct morphogenesis tissue morphogenesis anatomical structure morphogenesis mammary gland epithelium development morphogenesis of a branching structure morphogenesis of a branching epithelium monocyte homeostasis leukocyte homeostasis myeloid cell homeostasis positive regulation of protein metabolic process regulation of protein metabolic process primary metabolic process regulation of primary metabolic process protein metabolic process positive regulation of cell communication positive regulation of signal transduction 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 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 cell communication positive regulation of cytokine-mediated signaling pathway positive regulation of signaling regulation of animal organ morphogenesis regulation of odontogenesis of dentin-containing tooth regulation of odontogenesis odontogenesis of dentin-containing tooth odontogenesis positive regulation of odontogenesis positive regulation of odontogenesis of dentin-containing tooth positive regulation of animal organ morphogenesis regulation of anatomical structure morphogenesis ossification regulation of ossification macrophage derived foam cell differentiation foam cell differentiation regulation of macrophage derived foam cell differentiation positive regulation of macrophage derived foam cell differentiation small GTPase-mediated signal transduction Ras protein signal transduction intracellular signal transduction intracellular signaling cassette developmental growth mammary duct terminal end bud growth growth developmental growth involved in morphogenesis macrophage homeostasis 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 macrophage proliferation glial cell proliferation neutrophil homeostasis osteoclast differentiation reproductive process developmental process involved in reproduction inflammatory response regulation of small GTPase mediated signal transduction regulation of intracellular signal transduction regulation of Ras protein signal transduction positive regulation of 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	CSF1-CSF1R complex protein-containing complex cellular anatomical structure intracellular anatomical structure perinuclear region of cytoplasm cytoplasm extracellular region extracellular space cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen CSF1-CSF1R complex protein-containing complex cellular anatomical structure intracellular anatomical structure perinuclear region of cytoplasm cytoplasm extracellular region extracellular space cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
C [auth X]	Macrophage colony-stimulating factor 1 receptor	molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity collagen receptor activity protein tyrosine kinase collagen receptor activity GPI-linked ephrin receptor activity protein-hormone receptor activity insulin receptor activity histone H3Y41 kinase activity histone H3 kinase activity histone modifying activity histone kinase activity placental growth factor receptor activity protein phosphatase binding phosphatase binding protein binding binding enzyme binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding platelet-derived growth factor beta-receptor activity platelet-derived growth factor receptor activity stem cell factor receptor activity brain-derived neurotrophic factor receptor activity neurotrophin receptor activity insulin-like growth factor receptor activity hepatocyte growth factor receptor activity boss receptor activity epidermal growth factor receptor activity macrophage colony-stimulating factor receptor activity platelet-derived growth factor alpha-receptor activity cytokine binding identical protein binding protein homodimerization activity protein dimerization activity fibroblast growth factor receptor activity vascular endothelial growth factor receptor activity histone H2AXY142 kinase activity histone H2AX kinase activity	response to peptide response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus 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 peptide response to stimulus response to chemical response to cytokine cellular response to cytokine stimulus response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus 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 immune system process defense response to other organism innate immune response response to external biotic stimulus multicellular organismal process regulation of biological process homeostatic process regulation of bone remodeling biological regulation tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis regulation of multicellular organismal process protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process cellular response to stimulus positive regulation of locomotion regulation of cell motility regulation of cellular process macrophage migration positive regulation of chemotaxis positive regulation of cell migration taxis cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of macrophage migration positive regulation of leukocyte chemotaxis granulocyte migration leukocyte migration regulation of response to stimulus regulation of locomotion regulation of response to external stimulus macrophage chemotaxis positive regulation of biological process positive regulation of response to stimulus regulation of granulocyte chemotaxis regulation of macrophage migration positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration myeloid leukocyte migration positive regulation of mononuclear cell migration cell motility locomotion positive regulation of cellular process cell chemotaxis regulation of macrophage chemotaxis positive regulation of leukocyte migration regulation of chemotaxis cellular response to chemical stimulus granulocyte chemotaxis mononuclear cell migration positive regulation of macrophage chemotaxis leukocyte chemotaxis positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of chemokine production regulation of gene expression biosynthetic process positive regulation of gene expression chemokine production positive regulation of chemokine production positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process modulation by host of viral process viral process positive regulation by host of viral process modulation of process of another organism host-mediated perturbation of symbiont process cellular component organization plasma membrane bounded cell projection organization ruffle organization cell projection organization cellular component organization or biogenesis developmental process head development olfactory lobe development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development olfactory bulb development telencephalon development system development positive regulation of cell communication positive regulation of signal transduction signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling 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 regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cytoskeleton organization regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction cellular developmental process forebrain generation of neurons generation of neurons central nervous system neuron differentiation neurogenesis neuron differentiation cell differentiation forebrain neuron differentiation regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation regulation of leukocyte proliferation leukocyte proliferation macrophage proliferation positive regulation of leukocyte proliferation positive regulation of macrophage proliferation regulation of macrophage proliferation axonogenesis plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell projection morphogenesis neuron projection morphogenesis axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development negative regulation of cell population proliferation positive regulation of phosphorylation positive regulation of phosphate metabolic process regulation of primary metabolic process regulation of phosphate metabolic process positive regulation of protein phosphorylation tyrosine phosphorylation of STAT protein positive regulation of phosphorus metabolic process regulation of protein metabolic process regulation of phosphorus metabolic process cell surface receptor signaling pathway via STAT regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process cell surface receptor signaling pathway regulation of tyrosine phosphorylation of STAT protein regulation of peptidyl-tyrosine phosphorylation positive regulation of tyrosine phosphorylation of STAT protein regulation of phosphorylation cell surface receptor signaling pathway via JAK-STAT cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway macrophage colony-stimulating factor signaling pathway cytokine-mediated signaling pathway cell junction maintenance cell junction organization cellular component maintenance cell-cell junction maintenance cell-cell junction organization microglial cell proliferation gliogenesis glial cell proliferation myeloid leukocyte differentiation hemopoiesis myeloid cell differentiation osteoclast differentiation leukocyte differentiation inflammatory response	cellular anatomical structure membrane CSF1-CSF1R complex protein-containing complex cell surface cell periphery plasma membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure membrane CSF1-CSF1R complex protein-containing complex cell surface cell periphery plasma membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR008001	Macrophage colony stimulating factor-1	Family
A, B	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily
C [auth X]	IPR001824	Tyrosine-protein kinase, receptor class III, conserved site	Conserved Site
C [auth X]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth X]	IPR008266	Tyrosine-protein kinase, active site	Active Site
C [auth X]	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
C [auth X]	IPR000719	Protein kinase domain	Domain
C [auth X]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth X]	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
C [auth X]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth X]	IPR007110	Immunoglobulin-like domain	Domain
C [auth X]	IPR017441	Protein kinase, ATP binding site	Binding Site
C [auth X]	IPR003598	Immunoglobulin subtype 2	Domain
C [auth X]	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
C [auth X]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C [auth X]	IPR050122	Receptor Tyrosine Kinase	Family
C [auth X]	IPR030658	Macrophage colony-stimulating factor 1 receptor	Family

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.