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Protein

Platelet-derived growth factor receptor beta

Gene

PDGFRB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Tyrosine-protein kinase that acts as cell-surface receptor for homodimeric PDGFB and PDGFD and for heterodimers formed by PDGFA and PDGFB, and plays an essential role in the regulation of embryonic development, cell proliferation, survival, differentiation, chemotaxis and migration. Plays an essential role in blood vessel development by promoting proliferation, migration and recruitment of pericytes and smooth muscle cells to endothelial cells. Plays a role in the migration of vascular smooth muscle cells and the formation of neointima at vascular injury sites. Required for normal development of the cardiovascular system. Required for normal recruitment of pericytes (mesangial cells) in the kidney glomerulus, and for normal formation of a branched network of capillaries in kidney glomeruli. Promotes rearrangement of the actin cytoskeleton and the formation of membrane ruffles. Binding of its cognate ligands - homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFD -leads to the activation of several signaling cascades; the response depends on the nature of the bound ligand and is modulated by the formation of heterodimers between PDGFRA and PDGFRB. Phosphorylates PLCG1, PIK3R1, PTPN11, RASA1/GAP, CBL, SHC1 and NCK1. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate, mobilization of cytosolic Ca2+ and the activation of protein kinase C. Phosphorylation of PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, leads to the activation of the AKT1 signaling pathway. Phosphorylation of SHC1, or of the C-terminus of PTPN11, creates a binding site for GRB2, resulting in the activation of HRAS, RAF1 and down-stream MAP kinases, including MAPK1/ERK2 and/or MAPK3/ERK1. Promotes phosphorylation and activation of SRC family kinases. Promotes phosphorylation of PDCD6IP/ALIX and STAM. Receptor signaling is down-regulated by protein phosphatases that dephosphorylate the receptor and its down-stream effectors, and by rapid internalization of the activated receptor.20 Publications

Catalytic activityi

ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate.PROSITE-ProRule annotation3 Publications

Enzyme regulationi

Present in an inactive conformation in the absence of bound ligand. Binding of PDGFB and/or PDGFD leads to dimerization and activation by autophosphorylation on tyrosine residues. Inhibited by imatinib.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei527 – 528Breakpoint for insertion to form PDE4DIP-PDGFRB fusion protein2
Binding sitei634ATPCurated1
Active sitei826Proton acceptorPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi606 – 614ATPPROSITE-ProRule annotation9

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • enzyme binding Source: BHF-UCL
  • phosphatidylinositol-4,5-bisphosphate 3-kinase activity Source: Reactome
  • platelet activating factor receptor activity Source: ProtInc
  • platelet-derived growth factor-activated receptor activity Source: ProtInc
  • platelet-derived growth factor beta-receptor activity Source: UniProtKB
  • platelet-derived growth factor binding Source: UniProtKB
  • platelet-derived growth factor receptor binding Source: BHF-UCL
  • protein kinase binding Source: UniProtKB
  • protein tyrosine kinase activity Source: UniProtKB
  • Ras guanyl-nucleotide exchange factor activity Source: Reactome
  • receptor binding Source: UniProtKB
  • vascular endothelial growth factor binding Source: BHF-UCL

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Kinase, Receptor, Transferase, Tyrosine-protein kinase

Keywords - Biological processi

Chemotaxis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciZFISH:HS03710-MONOMER.
BRENDAi2.7.10.1. 2681.
ReactomeiR-HSA-1257604. PIP3 activates AKT signaling.
R-HSA-186763. Downstream signal transduction.
R-HSA-186797. Signaling by PDGF.
R-HSA-2219530. Constitutive Signaling by Aberrant PI3K in Cancer.
R-HSA-5673001. RAF/MAP kinase cascade.
R-HSA-6811558. PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling.
SignaLinkiP09619.
SIGNORiP09619.

Names & Taxonomyi

Protein namesi
Recommended name:
Platelet-derived growth factor receptor beta (EC:2.7.10.1)
Short name:
PDGF-R-beta
Short name:
PDGFR-beta
Alternative name(s):
Beta platelet-derived growth factor receptor
Beta-type platelet-derived growth factor receptor
CD140 antigen-like family member B
Platelet-derived growth factor receptor 1
Short name:
PDGFR-1
CD_antigen: CD140b
Gene namesi
Name:PDGFRB
Synonyms:PDGFR, PDGFR1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8804. PDGFRB.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini33 – 532ExtracellularSequence analysisAdd BLAST500
Transmembranei533 – 553HelicalSequence analysisAdd BLAST21
Topological domaini554 – 1106CytoplasmicSequence analysisAdd BLAST553

GO - Cellular componenti

  • apical plasma membrane Source: UniProtKB
  • cell surface Source: Ensembl
  • cytoplasm Source: UniProtKB
  • cytoplasmic, membrane-bounded vesicle Source: UniProtKB-SubCell
  • extracellular exosome Source: UniProtKB
  • focal adhesion Source: UniProtKB
  • integral component of membrane Source: UniProtKB-KW
  • intrinsic component of plasma membrane Source: UniProtKB
  • lysosomal lumen Source: UniProtKB-SubCell
  • membrane Source: UniProtKB
  • nucleus Source: UniProtKB
  • plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cytoplasmic vesicle, Lysosome, Membrane

Pathology & Biotechi

Involvement in diseasei

A chromosomal aberration involving PDGFRB is found in a form of chronic myelomonocytic leukemia (CMML). Translocation t(5;12)(q33;p13) with EVT6/TEL. It is characterized by abnormal clonal myeloid proliferation and by progression to acute myelogenous leukemia (AML).

Myeloproliferative disorder chronic with eosinophilia (MPE)
The gene represented in this entry may be involved in disease pathogenesis. Chromosomal aberrations involving PDGFRB have been found in many instances of chronic myeloproliferative disorder with eosinophilia. Translocation t(5;12) with ETV6 on chromosome 12 creating an PDGFRB-ETV6 fusion protein (PubMed:12181402). Translocation t(5;15)(q33;q22) with TP53BP1 creating a PDGFRB-TP53BP1 fusion protein (PubMed:15492236). Translocation t(1;5)(q23;q33) that forms a PDE4DIP-PDGFRB fusion protein (PubMed:12907457). Translocation t(5;6)(q33-34;q23) with CEP85L that fuses the 5'-end of CEP85L (isoform 4) to the 3'-end of PDGFRB (PubMed:21938754).4 Publications
Disease descriptionA hematologic disorder characterized by malignant eosinophils proliferation.
See also OMIM:131440
Leukemia, acute myelogenous (AML)
The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving PDGFRB has been found in a patient with AML. Translocation t(5;14)(q33;q32) with TRIP11 (PubMed:9373237).1 Publication
Disease descriptionA subtype of acute leukemia, a cancer of the white blood cells. AML is a malignant disease of bone marrow characterized by maturational arrest of hematopoietic precursors at an early stage of development. Clonal expansion of myeloid blasts occurs in bone marrow, blood, and other tissue. Myelogenous leukemias develop from changes in cells that normally produce neutrophils, basophils, eosinophils and monocytes.
See also OMIM:601626
Leukemia, juvenile myelomonocytic (JMML)
The gene represented in this entry may be involved in disease pathogenesis. A chromosomal aberration involving PDGFRB has been found in a patient with JMML. Translocation t(5;17)(q33;p11.2) with SPECC1 (PubMed:15087372).1 Publication
Disease descriptionAn aggressive pediatric myelodysplastic syndrome/myeloproliferative disorder characterized by malignant transformation in the hematopoietic stem cell compartment with proliferation of differentiated progeny. Patients have splenomegaly, enlarged lymph nodes, rashes, and hemorrhages.
See also OMIM:607785
Basal ganglia calcification, idiopathic, 4 (IBGC4)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of basal ganglia calcification, an autosomal dominant condition characterized by symmetric calcification in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms, including parkinsonism, dystonia, tremor, ataxia, dementia, psychosis, seizures, and chronic headache. Serum levels of calcium, phosphate, alkaline phosphatase and parathyroid hormone are normal. The neuropathological hallmark of the disease is vascular and pericapillary calcification, mainly of calcium phosphate, in the affected brain areas.
See also OMIM:615007
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_069320658L → P in IBGC4; no effect on protein abundance; loss of PDGF beta receptor activity. 3 PublicationsCorresponds to variant rs397509381dbSNPEnsembl.1
Natural variantiVAR_069321987R → W in IBGC4; decreased protein abundance; no effect on receptor activity; decreased PDGF signaling pathway. 3 PublicationsCorresponds to variant rs397509382dbSNPEnsembl.1
Natural variantiVAR_0753951071E → V in IBGC4; no effect on protein abundance; no effect on receptor activity; decreased PDGF signaling pathway. 2 Publications1
Myofibromatosis, infantile 1 (IMF1)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA rare mesenchymal disorder characterized by the development of benign tumors in the skin, striated muscles, bones, and, more rarely, visceral organs. Subcutaneous or soft tissue nodules commonly involve the skin of the head, neck, and trunk. Skeletal and muscular lesions occur in about half of the patients. Lesions may be solitary or multicentric, and they may be present at birth or become apparent in early infancy or occasionally in adult life. Visceral lesions are associated with high morbidity and mortality.
See also OMIM:228550
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_069925561R → C in IMF1. 1 PublicationCorresponds to variant rs367543286dbSNPEnsembl.1
Natural variantiVAR_069926660P → T in IMF1. 1 PublicationCorresponds to variant rs144050370dbSNPEnsembl.1
Kosaki overgrowth syndrome (KOGS)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA syndrome characterized by somatic overgrowth, distinctive facial features, hyperelastic and fragile skin, and progressive neurologic deterioration with white matter lesions on brain imaging.
See also OMIM:616592
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_075865584P → R in KOGS. 1 Publication1
Premature aging syndrome, Penttinen type (PENTT)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA syndrome characterized by a prematurely aged appearance with lipoatrophy, epidermal and dermal atrophy along with hypertrophic lesions that resemble scars, thin hair, proptosis, underdeveloped cheekbones, and marked acro-osteolysis.
See also OMIM:601812
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_075866665V → A in PENTT; gain of function in protein tyrosine kinase activity; shows ligand-independent constitutive signaling. 1 Publication1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi579Y → F: Loss of kinase activity; when associated with F-581. Strongly reduces interaction with SRC family kinases. No effect on interaction with GRB10. 2 Publications1
Mutagenesisi581Y → F: Loss of kinase activity; when associated with F-579. No effect on interaction with GRB10. 2 Publications1
Mutagenesisi634K → A or R: Loss of kinase activity. Abolishes interaction with RASA1. No effect on phosphatidylinositol 3-kinase activity. 3 Publications1
Mutagenesisi716Y → F: No effect neither on interaction with GRB10 and RASA1 nor on phosphatidylinositol 3-kinase activity. 2 Publications1
Mutagenesisi740Y → F: Strongly reduces up-regulation of cell proliferation; when associated with F-751. Strongly decreases phosphatidylinositol 3-kinase activity. No effect on interaction with GRB10 and RASA1. 4 Publications1
Mutagenesisi751Y → F: Strongly reduces up-regulation of cell proliferation; when associated with F-740. Abolishes phosphatidylinositol 3-kinase activity and interaction with NCK1, and slightly reduces interaction with RASA1. No effect on interaction with GRB10. 6 Publications1
Mutagenesisi763Y → F: No effect on interaction with RASA1 and on phosphatidylinositol 3-kinase activity. 1 Publication1
Mutagenesisi771Y → F: Loss of interaction with GRB10. Abolishes interaction with RASA1. No effect on phosphatidylinositol 3-kinase activity. 3 Publications1
Mutagenesisi775Y → F: No effect on interaction with RASA1 and on phosphatidylinositol 3-kinase activity. 1 Publication1
Mutagenesisi778Y → F: Strongly reduces expression levels. 1 Publication1
Mutagenesisi857Y → F: Reduces kinase activity. No effect on interaction with GRB10. Abolishes interaction with RASA1. No effect on phosphatidylinositol 3-kinase activity. 4 Publications1
Mutagenesisi1009Y → F: No effect on interaction with GRB10. Abolishes interaction with PLCG1; when associated with F-1021. 3 Publications1
Mutagenesisi1021Y → F: Strongly reduces up-regulation of cell proliferation. Abolishes interaction with PLCG1; when associated with F-1009. No effect on interaction with GRB10. 4 Publications1

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei527 – 528Breakpoint for translocation to form TRIP11-PDGFRB2
Sitei558 – 559Breakpoint for translocation to form the CEP85L-PDGFRB fusion protein2

Keywords - Diseasei

Disease mutation, Proto-oncogene

Organism-specific databases

DisGeNETi5159.
MalaCardsiPDGFRB.
MIMi131440. phenotype.
228550. phenotype.
601626. phenotype.
601812. phenotype.
607785. phenotype.
615007. phenotype.
616592. phenotype.
OpenTargetsiENSG00000113721.
Orphaneti1980. Bilateral striopallidodentate calcinosis.
98823. Chronic myelomonocytic leukemia.
2591. Infantile myofibromatosis.
168950. Myeloid neoplasm associated with PDGFRB rearrangement.
314950. Primary hypereosinophilic syndrome.
86830. Unclassified chronic myeloproliferative disease.
PharmGKBiPA33148.

Chemistry databases

ChEMBLiCHEMBL1913.
DrugBankiDB00102. Becaplermin.
DB01254. Dasatinib.
DB00619. Imatinib.
DB06589. Pazopanib.
DB08896. Regorafenib.
DB00398. Sorafenib.
DB01268. Sunitinib.
GuidetoPHARMACOLOGYi1804.

Polymorphism and mutation databases

BioMutaiPDGFRB.
DMDMi129890.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 321 PublicationAdd BLAST32
ChainiPRO_000001675733 – 1106Platelet-derived growth factor receptor betaAdd BLAST1074

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi45N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi54 ↔ 100PROSITE-ProRule annotation1 Publication
Glycosylationi89N-linked (GlcNAc...)1 Publication1
Glycosylationi103N-linked (GlcNAc...)1 Publication1
Disulfide bondi149 ↔ 190PROSITE-ProRule annotation1 Publication
Glycosylationi215N-linked (GlcNAc...)1 Publication1
Glycosylationi230N-linked (GlcNAc...)1 Publication1
Disulfide bondi235 ↔ 291PROSITE-ProRule annotation1 Publication
Glycosylationi292N-linked (GlcNAc...)1 Publication1
Glycosylationi307N-linked (GlcNAc...)1 Publication1
Glycosylationi354N-linked (GlcNAc...)Sequence analysis1
Glycosylationi371N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi436 ↔ 508PROSITE-ProRule annotation
Glycosylationi468N-linked (GlcNAc...)Sequence analysis1
Glycosylationi479N-linked (GlcNAc...)Sequence analysis1
Modified residuei562Phosphotyrosine; by autocatalysis1 Publication1
Modified residuei579Phosphotyrosine; by autocatalysis3 Publications1
Modified residuei581Phosphotyrosine; by autocatalysis2 Publications1
Modified residuei686Phosphotyrosine; by ABL1 and ABL2By similarity1
Modified residuei716Phosphotyrosine; by autocatalysis1 Publication1
Modified residuei740Phosphotyrosine; by autocatalysis2 Publications1
Modified residuei751Phosphotyrosine; by autocatalysis5 Publications1
Modified residuei763Phosphotyrosine; by autocatalysis1 Publication1
Modified residuei771Phosphotyrosine; by autocatalysis4 Publications1
Modified residuei775Phosphotyrosine; by autocatalysis1 Publication1
Modified residuei778Phosphotyrosine; by autocatalysis1 Publication1
Modified residuei857Phosphotyrosine; by autocatalysis5 Publications1
Modified residuei934Phosphotyrosine; by ABL1 and ABL2By similarity1
Modified residuei970Phosphotyrosine; by ABL1 and ABL2By similarity1
Modified residuei1009Phosphotyrosine; by autocatalysis3 Publications1
Modified residuei1021Phosphotyrosine; by autocatalysis4 Publications1

Post-translational modificationi

Autophosphorylated on tyrosine residues upon ligand binding. Autophosphorylation occurs in trans, i.e. one subunit of the dimeric receptor phosphorylates tyrosine residues on the other subunit. Phosphorylation at Tyr-579, and to a lesser degree, at Tyr-581, is important for interaction with SRC family kinases. Phosphorylation at Tyr-740 and Tyr-751 is important for interaction with PIK3R1. Phosphorylation at Tyr-751 is important for interaction with NCK1. Phosphorylation at Tyr-771 and Tyr-857 is important for interaction with RASA1/GAP. Phosphorylation at Tyr-857 is important for efficient phosphorylation of PLCG1 and PTPN11, resulting in increased phosphorylation of AKT1, MAPK1/ERK2 and/or MAPK3/ERK1, PDCD6IP/ALIX and STAM, and in increased cell proliferation. Phosphorylation at Tyr-1009 is important for interaction with PTPN11. Phosphorylation at Tyr-1009 and Tyr-1021 is important for interaction with PLCG1. Phosphorylation at Tyr-1021 is important for interaction with CBL; PLCG1 and CBL compete for the same binding site. Dephosphorylated by PTPRJ at Tyr-751, Tyr-857, Tyr-1009 and Tyr-1021. Dephosphorylated by PTPN2 at Tyr-579 and Tyr-1021.8 Publications
N-glycosylated.2 Publications
Ubiquitinated. After autophosphorylation, the receptor is polyubiquitinated, leading to its degradation.2 Publications

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiP09619.
MaxQBiP09619.
PaxDbiP09619.
PeptideAtlasiP09619.
PRIDEiP09619.

PTM databases

iPTMnetiP09619.
PhosphoSitePlusiP09619.

Expressioni

Gene expression databases

BgeeiENSG00000113721.
CleanExiHS_PDGFRB.
ExpressionAtlasiP09619. baseline and differential.
GenevisibleiP09619. HS.

Organism-specific databases

HPAiCAB003842.
CAB018144.
HPA028499.

Interactioni

Subunit structurei

Interacts with homodimeric PDGFB and PDGFD, and with heterodimers formed by PDGFA and PDGFB. May also interact with homodimeric PDGFC. Monomer in the absence of bound ligand. Interaction with homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFD, leads to receptor dimerization, where both PDGFRA homodimers and heterodimers with PDGFRB are observed. Interacts with SH2B2/APS. Interacts directly (tyrosine phosphorylated) with SHB. Interacts (tyrosine phosphorylated) with PIK3R1 and RASA1. Interacts (tyrosine phosphorylated) with CBL. Interacts (tyrosine phosphorylated) with SRC and SRC family kinases. Interacts (tyrosine phosphorylated) with PIK3C2B, maybe indirectly. Interacts (tyrosine phosphorylated) with SHC1, GRB7, GRB10 and NCK1. Interaction with GRB2 is mediated by SHC1. Interacts (via C-terminus) with SLC9A3R1.20 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
E5P0CK452EBI-641237,EBI-7015490From a different organism.
FYNP062413EBI-641237,EBI-515315
GRB7Q144514EBI-641237,EBI-970191
KLHL12Q53G595EBI-641237,EBI-740929
PDGFBP0112713EBI-641237,EBI-1554925
PIK3R1P237276EBI-641237,EBI-520244From a different organism.
PIK3R1P2798619EBI-641237,EBI-79464
PLCG1P084873EBI-641237,EBI-8013886From a different organism.
PLCG1P191745EBI-641237,EBI-79387
PTENP604843EBI-641237,EBI-696162
PTPN1P180313EBI-641237,EBI-968788
PTPN11Q061248EBI-641237,EBI-297779
PTPN12Q052093EBI-641237,EBI-2266035
PTPRJQ129134EBI-641237,EBI-2264500
RAF1P040492EBI-641237,EBI-365996
RASA1P209363EBI-641237,EBI-1026476
SLAQ132394EBI-641237,EBI-726214
SLC9A3R1O147455EBI-641237,EBI-349787
TRIP6Q156543EBI-641237,EBI-742327
V-SRCP250204EBI-641237,EBI-8636140From a different organism.

GO - Molecular functioni

  • enzyme binding Source: BHF-UCL
  • platelet-derived growth factor binding Source: UniProtKB
  • platelet-derived growth factor receptor binding Source: BHF-UCL
  • protein kinase binding Source: UniProtKB
  • receptor binding Source: UniProtKB
  • vascular endothelial growth factor binding Source: BHF-UCL

Protein-protein interaction databases

BioGridi111185. 73 interactors.
DIPiDIP-558N.
IntActiP09619. 79 interactors.
MINTiMINT-148093.
STRINGi9606.ENSP00000261799.

Chemistry databases

BindingDBiP09619.

Structurei

Secondary structure

11106
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi40 – 43Combined sources4
Beta strandi50 – 58Combined sources9
Beta strandi61 – 64Combined sources4
Beta strandi70 – 75Combined sources6
Beta strandi81 – 87Combined sources7
Helixi92 – 94Combined sources3
Beta strandi96 – 101Combined sources6
Beta strandi114 – 119Combined sources6
Helixi132 – 135Combined sources4
Beta strandi136 – 141Combined sources6
Beta strandi145 – 147Combined sources3
Beta strandi158 – 164Combined sources7
Turni175 – 177Combined sources3
Beta strandi178 – 181Combined sources4
Beta strandi185 – 194Combined sources10
Beta strandi197 – 200Combined sources4
Beta strandi204 – 208Combined sources5
Beta strandi217 – 221Combined sources5
Beta strandi223 – 226Combined sources4
Beta strandi231 – 239Combined sources9
Beta strandi241 – 248Combined sources8
Beta strandi252 – 255Combined sources4
Beta strandi261 – 265Combined sources5
Turni267 – 270Combined sources4
Beta strandi271 – 280Combined sources10
Beta strandi287 – 295Combined sources9
Turni296 – 299Combined sources4
Beta strandi300 – 311Combined sources12
Helixi530 – 556Combined sources27

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GQ5X-ray2.20A1102-1106[»]
1H9OX-ray1.79B751-755[»]
1LWPmodel-A600-962[»]
1SHAX-ray1.50B751-755[»]
2L6WNMR-A/B526-563[»]
2PLDNMR-B1018-1029[»]
2PLENMR-B1018-1029[»]
3MJGX-ray2.30X/Y33-314[»]
ProteinModelPortaliP09619.
SMRiP09619.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP09619.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini33 – 120Ig-like C2-type 1Add BLAST88
Domaini129 – 210Ig-like C2-type 2Add BLAST82
Domaini214 – 309Ig-like C2-type 3Add BLAST96
Domaini331 – 403Ig-like C2-type 4Add BLAST73
Domaini416 – 524Ig-like C2-type 5Add BLAST109
Domaini600 – 962Protein kinasePROSITE-ProRule annotationAdd BLAST363

Sequence similaritiesi

Belongs to the protein kinase superfamily. Tyr protein kinase family. CSF-1/PDGF receptor subfamily.PROSITE-ProRule annotation
Contains 1 protein kinase domain.PROSITE-ProRule annotation

Keywords - Domaini

Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG0200. Eukaryota.
COG0515. LUCA.
GeneTreeiENSGT00760000118923.
HOGENOMiHOG000112009.
HOVERGENiHBG004335.
InParanoidiP09619.
KOiK05089.
OMAiAPYDNYV.
OrthoDBiEOG091G01TL.
PhylomeDBiP09619.
TreeFamiTF325768.

Family and domain databases

Gene3Di2.60.40.10. 7 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR013151. Immunoglobulin.
IPR011009. Kinase-like_dom.
IPR027288. PGFRB.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR001245. Ser-Thr/Tyr_kinase_cat_dom.
IPR008266. Tyr_kinase_AS.
IPR020635. Tyr_kinase_cat_dom.
IPR016243. Tyr_kinase_CSF1/PDGF_rcpt.
IPR001824. Tyr_kinase_rcpt_3_CS.
[Graphical view]
PANTHERiPTHR24416:SF53. PTHR24416:SF53. 3 hits.
PfamiPF07679. I-set. 1 hit.
PF00047. ig. 1 hit.
PF07714. Pkinase_Tyr. 1 hit.
[Graphical view]
PIRSFiPIRSF500948. Beta-PDGF_receptor. 1 hit.
PIRSF000615. TyrPK_CSF1-R. 1 hit.
SMARTiSM00409. IG. 3 hits.
SM00408. IGc2. 3 hits.
SM00219. TyrKc. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 3 hits.
SSF56112. SSF56112. 2 hits.
PROSITEiPS50835. IG_LIKE. 2 hits.
PS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00109. PROTEIN_KINASE_TYR. 1 hit.
PS00240. RECEPTOR_TYR_KIN_III. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P09619-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

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MRLPGAMPAL ALKGELLLLS LLLLLEPQIS QGLVVTPPGP ELVLNVSSTF
60 70 80 90 100
VLTCSGSAPV VWERMSQEPP QEMAKAQDGT FSSVLTLTNL TGLDTGEYFC
110 120 130 140 150
THNDSRGLET DERKRLYIFV PDPTVGFLPN DAEELFIFLT EITEITIPCR
160 170 180 190 200
VTDPQLVVTL HEKKGDVALP VPYDHQRGFS GIFEDRSYIC KTTIGDREVD
210 220 230 240 250
SDAYYVYRLQ VSSINVSVNA VQTVVRQGEN ITLMCIVIGN EVVNFEWTYP
260 270 280 290 300
RKESGRLVEP VTDFLLDMPY HIRSILHIPS AELEDSGTYT CNVTESVNDH
310 320 330 340 350
QDEKAINITV VESGYVRLLG EVGTLQFAEL HRSRTLQVVF EAYPPPTVLW
360 370 380 390 400
FKDNRTLGDS SAGEIALSTR NVSETRYVSE LTLVRVKVAE AGHYTMRAFH
410 420 430 440 450
EDAEVQLSFQ LQINVPVRVL ELSESHPDSG EQTVRCRGRG MPQPNIIWSA
460 470 480 490 500
CRDLKRCPRE LPPTLLGNSS EEESQLETNV TYWEEEQEFE VVSTLRLQHV
510 520 530 540 550
DRPLSVRCTL RNAVGQDTQE VIVVPHSLPF KVVVISAILA LVVLTIISLI
560 570 580 590 600
ILIMLWQKKP RYEIRWKVIE SVSSDGHEYI YVDPMQLPYD STWELPRDQL
610 620 630 640 650
VLGRTLGSGA FGQVVEATAH GLSHSQATMK VAVKMLKSTA RSSEKQALMS
660 670 680 690 700
ELKIMSHLGP HLNVVNLLGA CTKGGPIYII TEYCRYGDLV DYLHRNKHTF
710 720 730 740 750
LQHHSDKRRP PSAELYSNAL PVGLPLPSHV SLTGESDGGY MDMSKDESVD
760 770 780 790 800
YVPMLDMKGD VKYADIESSN YMAPYDNYVP SAPERTCRAT LINESPVLSY
810 820 830 840 850
MDLVGFSYQV ANGMEFLASK NCVHRDLAAR NVLICEGKLV KICDFGLARD
860 870 880 890 900
IMRDSNYISK GSTFLPLKWM APESIFNSLY TTLSDVWSFG ILLWEIFTLG
910 920 930 940 950
GTPYPELPMN EQFYNAIKRG YRMAQPAHAS DEIYEIMQKC WEEKFEIRPP
960 970 980 990 1000
FSQLVLLLER LLGEGYKKKY QQVDEEFLRS DHPAILRSQA RLPGFHGLRS
1010 1020 1030 1040 1050
PLDTSSVLYT AVQPNEGDND YIIPLPDPKP EVADEGPLEG SPSLASSTLN
1060 1070 1080 1090 1100
EVNTSSTISC DSPLEPQDEP EPEPQLELQV EPEPELEQLP DSGCPAPRAE

AEDSFL
Length:1,106
Mass (Da):123,968
Last modified:July 1, 1989 - v1
Checksum:i038C15E531D6E89D
GO
Isoform 2 (identifier: P09619-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     311-336: VESGYVRLLGEVGTLQFAELHRSRTL → RAATCGSWERWAHYNLLSCIGAGHCR
     337-1106: Missing.

Show »
Length:336
Mass (Da):37,412
Checksum:i5BEDAFC416865068
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti241E → D in AAA36427 (PubMed:2850496).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_03437729I → F.1 PublicationCorresponds to variant rs17110944dbSNPEnsembl.1
Natural variantiVAR_035125180S → F.1 PublicationCorresponds to variant rs17853027dbSNPEnsembl.1
Natural variantiVAR_042027282E → K.1 PublicationCorresponds to variant rs34586048dbSNPEnsembl.1
Natural variantiVAR_049717345P → S.Corresponds to variant rs2229558dbSNPEnsembl.1
Natural variantiVAR_042028485E → K.1 PublicationCorresponds to variant rs41287110dbSNPEnsembl.1
Natural variantiVAR_069925561R → C in IMF1. 1 PublicationCorresponds to variant rs367543286dbSNPEnsembl.1
Natural variantiVAR_075865584P → R in KOGS. 1 Publication1
Natural variantiVAR_042029589Y → H in a gastric adenocarcinoma sample; somatic mutation. 1 Publication1
Natural variantiVAR_069320658L → P in IBGC4; no effect on protein abundance; loss of PDGF beta receptor activity. 3 PublicationsCorresponds to variant rs397509381dbSNPEnsembl.1
Natural variantiVAR_069926660P → T in IMF1. 1 PublicationCorresponds to variant rs144050370dbSNPEnsembl.1
Natural variantiVAR_075866665V → A in PENTT; gain of function in protein tyrosine kinase activity; shows ligand-independent constitutive signaling. 1 Publication1
Natural variantiVAR_042030718N → Y.1 PublicationCorresponds to variant rs35322465dbSNPEnsembl.1
Natural variantiVAR_042031882T → I in a breast infiltrating ductal carcinoma sample; somatic mutation. 1 Publication1
Natural variantiVAR_069321987R → W in IBGC4; decreased protein abundance; no effect on receptor activity; decreased PDGF signaling pathway. 3 PublicationsCorresponds to variant rs397509382dbSNPEnsembl.1
Natural variantiVAR_0753951071E → V in IBGC4; no effect on protein abundance; no effect on receptor activity; decreased PDGF signaling pathway. 2 Publications1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_056008311 – 336VESGY…RSRTL → RAATCGSWERWAHYNLLSCI GAGHCR in isoform 2. 1 PublicationAdd BLAST26
Alternative sequenceiVSP_056009337 – 1106Missing in isoform 2. 1 PublicationAdd BLAST770

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03278 mRNA. Translation: AAA60049.1.
M21616 mRNA. Translation: AAA36427.1.
EU826595 mRNA. Translation: ACF47631.1.
AC005895 Genomic DNA. No translation available.
AC011382 Genomic DNA. No translation available.
BC032224 mRNA. Translation: AAH32224.1.
U33172 Genomic DNA. Translation: AAC51675.1.
CCDSiCCDS4303.1. [P09619-1]
PIRiA28206. PFHUGB.
RefSeqiNP_002600.1. NM_002609.3. [P09619-1]
XP_011535960.1. XM_011537658.1. [P09619-1]
XP_011535961.1. XM_011537659.1. [P09619-1]
UniGeneiHs.509067.

Genome annotation databases

EnsembliENST00000261799; ENSP00000261799; ENSG00000113721. [P09619-1]
GeneIDi5159.
KEGGihsa:5159.
UCSCiuc003lro.4. human. [P09619-1]

Keywords - Coding sequence diversityi

Alternative splicing, Chromosomal rearrangement, Polymorphism

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03278 mRNA. Translation: AAA60049.1.
M21616 mRNA. Translation: AAA36427.1.
EU826595 mRNA. Translation: ACF47631.1.
AC005895 Genomic DNA. No translation available.
AC011382 Genomic DNA. No translation available.
BC032224 mRNA. Translation: AAH32224.1.
U33172 Genomic DNA. Translation: AAC51675.1.
CCDSiCCDS4303.1. [P09619-1]
PIRiA28206. PFHUGB.
RefSeqiNP_002600.1. NM_002609.3. [P09619-1]
XP_011535960.1. XM_011537658.1. [P09619-1]
XP_011535961.1. XM_011537659.1. [P09619-1]
UniGeneiHs.509067.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GQ5X-ray2.20A1102-1106[»]
1H9OX-ray1.79B751-755[»]
1LWPmodel-A600-962[»]
1SHAX-ray1.50B751-755[»]
2L6WNMR-A/B526-563[»]
2PLDNMR-B1018-1029[»]
2PLENMR-B1018-1029[»]
3MJGX-ray2.30X/Y33-314[»]
ProteinModelPortaliP09619.
SMRiP09619.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111185. 73 interactors.
DIPiDIP-558N.
IntActiP09619. 79 interactors.
MINTiMINT-148093.
STRINGi9606.ENSP00000261799.

Chemistry databases

BindingDBiP09619.
ChEMBLiCHEMBL1913.
DrugBankiDB00102. Becaplermin.
DB01254. Dasatinib.
DB00619. Imatinib.
DB06589. Pazopanib.
DB08896. Regorafenib.
DB00398. Sorafenib.
DB01268. Sunitinib.
GuidetoPHARMACOLOGYi1804.

PTM databases

iPTMnetiP09619.
PhosphoSitePlusiP09619.

Polymorphism and mutation databases

BioMutaiPDGFRB.
DMDMi129890.

Proteomic databases

EPDiP09619.
MaxQBiP09619.
PaxDbiP09619.
PeptideAtlasiP09619.
PRIDEiP09619.

Protocols and materials databases

DNASUi5159.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000261799; ENSP00000261799; ENSG00000113721. [P09619-1]
GeneIDi5159.
KEGGihsa:5159.
UCSCiuc003lro.4. human. [P09619-1]

Organism-specific databases

CTDi5159.
DisGeNETi5159.
GeneCardsiPDGFRB.
GeneReviewsiPDGFRB.
HGNCiHGNC:8804. PDGFRB.
HPAiCAB003842.
CAB018144.
HPA028499.
MalaCardsiPDGFRB.
MIMi131440. phenotype.
173410. gene.
228550. phenotype.
601626. phenotype.
601812. phenotype.
607785. phenotype.
615007. phenotype.
616592. phenotype.
neXtProtiNX_P09619.
OpenTargetsiENSG00000113721.
Orphaneti1980. Bilateral striopallidodentate calcinosis.
98823. Chronic myelomonocytic leukemia.
2591. Infantile myofibromatosis.
168950. Myeloid neoplasm associated with PDGFRB rearrangement.
314950. Primary hypereosinophilic syndrome.
86830. Unclassified chronic myeloproliferative disease.
PharmGKBiPA33148.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0200. Eukaryota.
COG0515. LUCA.
GeneTreeiENSGT00760000118923.
HOGENOMiHOG000112009.
HOVERGENiHBG004335.
InParanoidiP09619.
KOiK05089.
OMAiAPYDNYV.
OrthoDBiEOG091G01TL.
PhylomeDBiP09619.
TreeFamiTF325768.

Enzyme and pathway databases

BioCyciZFISH:HS03710-MONOMER.
BRENDAi2.7.10.1. 2681.
ReactomeiR-HSA-1257604. PIP3 activates AKT signaling.
R-HSA-186763. Downstream signal transduction.
R-HSA-186797. Signaling by PDGF.
R-HSA-2219530. Constitutive Signaling by Aberrant PI3K in Cancer.
R-HSA-5673001. RAF/MAP kinase cascade.
R-HSA-6811558. PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling.
SignaLinkiP09619.
SIGNORiP09619.

Miscellaneous databases

ChiTaRSiPDGFRB. human.
EvolutionaryTraceiP09619.
GeneWikiiPDGFRB.
GenomeRNAii5159.
PROiP09619.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000113721.
CleanExiHS_PDGFRB.
ExpressionAtlasiP09619. baseline and differential.
GenevisibleiP09619. HS.

Family and domain databases

Gene3Di2.60.40.10. 7 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR013151. Immunoglobulin.
IPR011009. Kinase-like_dom.
IPR027288. PGFRB.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR001245. Ser-Thr/Tyr_kinase_cat_dom.
IPR008266. Tyr_kinase_AS.
IPR020635. Tyr_kinase_cat_dom.
IPR016243. Tyr_kinase_CSF1/PDGF_rcpt.
IPR001824. Tyr_kinase_rcpt_3_CS.
[Graphical view]
PANTHERiPTHR24416:SF53. PTHR24416:SF53. 3 hits.
PfamiPF07679. I-set. 1 hit.
PF00047. ig. 1 hit.
PF07714. Pkinase_Tyr. 1 hit.
[Graphical view]
PIRSFiPIRSF500948. Beta-PDGF_receptor. 1 hit.
PIRSF000615. TyrPK_CSF1-R. 1 hit.
SMARTiSM00409. IG. 3 hits.
SM00408. IGc2. 3 hits.
SM00219. TyrKc. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 3 hits.
SSF56112. SSF56112. 2 hits.
PROSITEiPS50835. IG_LIKE. 2 hits.
PS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00109. PROTEIN_KINASE_TYR. 1 hit.
PS00240. RECEPTOR_TYR_KIN_III. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPGFRB_HUMAN
AccessioniPrimary (citable) accession number: P09619
Secondary accession number(s): B5A957, Q8N5L4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: November 30, 2016
This is version 209 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
  2. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. Human and mouse protein kinases
    Human and mouse protein kinases: classification and index
  8. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.