4LIQ

Structure of the extracellular domain of human CSF-1 receptor in complex with the Fab fragment of RG7155

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-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)
C [auth L]	d4liql2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d4liql1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d4liqh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth E]	I-set_4	e4liqE1	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)
A [auth E]	I-set_5	e4liqE5	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_5	ECOD (1.6)
A [auth E]	IG_like	e4liqE3	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)
A [auth E]	I-set_13	e4liqE4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_13	ECOD (1.6)
A [auth E]	I-set_2	e4liqE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_2	ECOD (1.6)
C [auth L]	C1-set_4	e4liqL2	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)
C [auth L]	V-set	e4liqL1	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	e4liqH1	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	e4liqH2	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)

Domain Annotation: CATH CATH Database Homepage

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

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
C [auth L]	RG7155 Fab	L-KAPPA	Humanized (humanized)	IGKV1-3901, IGKV1D-3901, IGKJ201, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B [auth H]	RG7155 Fab	VH-CH1	Humanized (humanized)	IGHV1-1801, IGHV1-1804, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L]	Light Chain	IGKV1	Kappa	macrophage colony-stimulating factor 1 receptor	SAbDab (2024-04-19)
B [auth H]	Heavy Chain	IGHV1	-	macrophage colony-stimulating factor 1 receptor	SAbDab (2024-04-19)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
C [auth L]	Emactuzumab	CSF1R/CD115/M-CSFR	Therapeutic SAbDab (2024-04-19)
B [auth H]	Emactuzumab	CSF1R/CD115/M-CSFR	Therapeutic SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E]	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain
A [auth E]	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-prot ...	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 [auth E]	Macrophage colony-stimulating factor 1 receptor	protein phosphatase binding phosphatase binding protein binding binding enzyme binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding protein phosphatase binding phosphatase binding protein binding binding enzyme binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding molecular transducer activity signaling receptor activity macrophage colony-stimulating factor receptor activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity growth factor binding cytokine binding identical protein binding protein homodimerization activity protein dimerization activity	cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular process cellular response to organic substance signal transduction response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus response to stress response to ischemia cell population proliferation regulation of signaling regulation of signal transduction regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette MAPK cascade regulation of cell communication 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 developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development multicellular organismal process epithelium development tube development mammary gland morphogenesis mammary gland development gland development animal organ development morphogenesis of an epithelium tissue development mammary gland duct morphogenesis tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis gland morphogenesis mammary gland epithelium development animal organ morphogenesis epithelial tube morphogenesis positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process primary metabolic process regulation of cellular metabolic process regulation of molecular function positive regulation of kinase activity regulation of protein tyrosine kinase activity regulation of kinase activity macromolecule modification metabolic process regulation of phosphorus metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process positive regulation of cellular metabolic process peptidyl-tyrosine modification positive regulation of molecular function positive regulation of protein modification process positive regulation of peptidyl-tyrosine phosphorylation organic substance metabolic process protein metabolic process positive regulation of protein kinase activity positive regulation of cellular process organonitrogen compound metabolic process positive regulation of transferase activity positive regulation of protein tyrosine kinase activity regulation of peptidyl-tyrosine phosphorylation positive regulation of catalytic activity regulation of macromolecule metabolic process regulation of protein kinase activity regulation of phosphorylation peptidyl-tyrosine phosphorylation homeostatic process regulation of bone remodeling 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 autophosphorylation positive regulation of locomotion regulation of cell motility 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 positive regulation of macrophage migration regulation of leukocyte migration positive regulation of leukocyte chemotaxis granulocyte migration leukocyte migration regulation of locomotion regulation of response to external stimulus macrophage chemotaxis 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 cell chemotaxis regulation of macrophage chemotaxis positive regulation of leukocyte migration regulation of chemotaxis granulocyte chemotaxis mononuclear cell migration positive regulation of macrophage chemotaxis leukocyte chemotaxis cellular biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process regulation of cytokine production organic substance biosynthetic process cytokine production regulation of biosynthetic process gene expression macromolecule biosynthetic process regulation of chemokine production regulation of cellular biosynthetic process 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 positive regulation of cellular biosynthetic process modulation by host of viral process viral process modulation by host of symbiont process positive regulation by host of viral process biological process involved in interaction with symbiont biological process involved in symbiotic interaction cellular component organization plasma membrane bounded cell projection organization ruffle organization cell projection organization cellular component organization or biogenesis myeloid leukocyte differentiation mononuclear cell differentiation myeloid cell differentiation monocyte differentiation leukocyte differentiation head development olfactory lobe development forebrain development brain development nervous system development central nervous system development olfactory bulb development telencephalon development system development positive regulation of cell communication positive regulation of signal transduction positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade positive regulation of intracellular signal transduction 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 forebrain generation of neurons generation of neurons central nervous system neuron differentiation neurogenesis neuron differentiation forebrain neuron differentiation regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis positive regulation of cell population proliferation regulation of cell population proliferation regulation of leukocyte proliferation leukocyte proliferation macrophage proliferation positive regulation of leukocyte proliferation positive regulation of macrophage proliferation regulation of macrophage proliferation macrophage differentiation axonogenesis plasma membrane bounded cell projection morphogenesis 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 tyrosine phosphorylation of STAT protein cell surface receptor signaling pathway via STAT regulation of tyrosine phosphorylation of STAT protein positive regulation of tyrosine phosphorylation of STAT protein cell surface receptor signaling pathway via JAK-STAT macrophage colony-stimulating factor 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 osteoclast differentiation inflammatory response cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway	CSF1-CSF1R complex protein-containing complex receptor complex cell surface cellular anatomical entity cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle nucleus CSF1-CSF1R complex protein-containing complex receptor complex cell surface cellular anatomical entity cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
C [auth L]	Fab fragment RG7155 light chain	-	-	-
B [auth H]	Fab fragment RG7155 heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth E]	Pharos: P07333	hereditary diffuse leukoencephalopathy with axonal spheroids and pigmented glia cancer acute myeloid leukemia tenosynovial giant cell tumor Neoplasm Metastasis breast carcinoma large cell medulloblastoma leukoencephalopathy with vanishing white matter lung carcinoma myofascial pain syndrome adrenal cortex carcinoma neurodegenerative disease benign neoplasm Parkinson disease fibromyalgia hereditary diffuse leukoencephalopathy with axonal spheroids and pigmented glia cancer acute myeloid leukemia tenosynovial giant cell tumor Neoplasm Metastasis breast carcinoma large cell medulloblastoma leukoencephalopathy with vanishing white matter lung carcinoma myofascial pain syndrome adrenal cortex carcinoma neurodegenerative disease benign neoplasm Parkinson disease fibromyalgia hematopoietic and lymphoid system neoplasm intellectual disability leukodystrophy limb-girdle muscular dystrophy medulloblastoma astrocytic tumor ovarian cancer breast cancer pilocytic astrocytoma colorectal cancer squamous cell lung carcinoma gastrointestinal stromal tumor invasive ductal breast carcinoma myelodysplastic syndrome Becker muscular dystrophy renal cell carcinoma Duchenne muscular dystrophy subependymal giant cell astrocytoma glioblastoma IgA glomerulonephritis

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.