3UEZ | pdb_00003uez

Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine in complex with the viral receptor BARF1

External Resource: Annotation

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	4-helical cytokines	8037095	3001717	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	4-helical cytokines	8037095	3001717	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	4-helical cytokines	8037095	3001717	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	4-helical cytokines	8037095	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)
C	V-set_15	e3uezC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)
C	PHA03376	e3uezC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PHA03376	ECOD (1.6)
A	V-set_15	e3uezA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)
A	PHA03376	e3uezA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PHA03376	ECOD (1.6)
B	V-set_15	e3uezB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)
B	PHA03376	e3uezB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PHA03376	ECOD (1.6)
D	V-set_15	e3uezD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_15	ECOD (1.6)
D	PHA03376	e3uezD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PHA03376	ECOD (1.6)
E	CSF-1	e3uezE1	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)
F	CSF-1	e3uezF1	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)
G	CSF-1	e3uezG1	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)
H	CSF-1	e3uezH1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	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)
E	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
F	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
G	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
H	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	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, 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 (202510-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Secreted protein BARF1	identical protein binding protein binding binding	-	cellular anatomical structure extracellular region
E, F, G, H	Macrophage colony-stimulating factor 1	molecular transducer activity binding molecular function activator activity signaling receptor binding signaling receptor activity growth factor activity signaling receptor activator activity protein binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity identical protein binding cytokine receptor binding macrophage colony-stimulating factor receptor binding molecular transducer activity binding molecular function activator activity signaling receptor binding signaling receptor activity growth factor activity signaling receptor activator activity protein binding molecular function regulator activity signaling receptor regulator activity receptor ligand 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 macrophage derived foam cell differentiation foam cell differentiation regulation of macrophage derived foam cell differentiation 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 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 monocyte activation cell activation myeloid leukocyte activation leukocyte activation 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	cellular anatomical structure membrane CSF1-CSF1R complex protein-containing complex membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle cellular anatomical structure membrane CSF1-CSF1R complex protein-containing complex membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm perinuclear region of cytoplasm extracellular region extracellular space cell periphery plasma membrane nucleus nuclear body nucleoplasm nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
E, F, G, H	IPR008001	Macrophage colony stimulating factor-1	Family
E, F, G, H	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: P09603	bone Paget disease malignant mesothelioma breast carcinoma attention deficit hyperactivity disorder, inattentive type glioblastoma lung carcinoma Malignant neoplasm of breast medulloblastoma tenosynovial giant cell tumor cancer large cell medulloblastoma malignant glioma pilocytic astrocytoma breast cancer chronic obstructive pulmonary disease bone Paget disease malignant mesothelioma breast carcinoma attention deficit hyperactivity disorder, inattentive type glioblastoma lung carcinoma Malignant neoplasm of breast medulloblastoma tenosynovial giant cell tumor cancer large cell medulloblastoma malignant glioma pilocytic astrocytoma breast cancer chronic obstructive pulmonary disease lung cancer psoriasis

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.