PDGFRB
Platelet-derived growth factor receptor beta
Also known as: CD140b, JTK12, PDGFR, PDGFR1, PGFRB_HUMAN
Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene
Protein identityUniProt · HPA
- UniProt accession
- P09619
- Gene
- PDGFRB
- Ensembl
- ENSG00000113721
- Chromosome
- 5
- Canonical length
- 1106 aa
- Protein class
- Cancer-related genes, CD markers, Disease related genes, Enzymes, FDA approved drug targets, Human disease related genes, Plasma proteins, Predicted intracellular proteins, Predicted membrane proteins, RAS pathway related proteins, Transporters
- Subcellular location
- Golgi apparatus,Vesicles
- Quaternary structure
- Homodimer
OverviewNCBI Gene
The protein encoded by this gene is a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor family. These growth factors are mitogens for cells of mesenchymal origin. The identity of the growth factor bound to a receptor monomer determines whether the functional receptor is a homodimer (PDGFB or PDGFD) or a heterodimer (PDGFA and PDGFB). This gene is essential for normal development of the cardiovascular system and aids in rearrangement of the actin cytoskeleton. This gene is flanked on chromosome 5 by the genes for granulocyte-macrophage colony-stimulating factor and macrophage-colony stimulating factor receptor; all three genes may be implicated in the 5-q syndrome. A translocation between chromosomes 5 and 12, that fuses this gene to that of the ETV6 gene, results in chronic myeloproliferative disorder with eosinophilia. [provided by RefSeq, Aug 2017]
Canonical amino-acid sequenceUniProt
1106 residues, UniProt reviewed canonical sequence.
>P09619|PDGFRB
1 MRLPGAMPAL ALKGELLLLS LLLLLEPQIS QGLVVTPPGP ELVLNVSSTF VLTCSGSAPV
61 VWERMSQEPP QEMAKAQDGT FSSVLTLTNL TGLDTGEYFC THNDSRGLET DERKRLYIFV
121 PDPTVGFLPN DAEELFIFLT EITEITIPCR VTDPQLVVTL HEKKGDVALP VPYDHQRGFS
181 GIFEDRSYIC KTTIGDREVD SDAYYVYRLQ VSSINVSVNA VQTVVRQGEN ITLMCIVIGN
241 EVVNFEWTYP RKESGRLVEP VTDFLLDMPY HIRSILHIPS AELEDSGTYT CNVTESVNDH
301 QDEKAINITV VESGYVRLLG EVGTLQFAEL HRSRTLQVVF EAYPPPTVLW FKDNRTLGDS
361 SAGEIALSTR NVSETRYVSE LTLVRVKVAE AGHYTMRAFH EDAEVQLSFQ LQINVPVRVL
421 ELSESHPDSG EQTVRCRGRG MPQPNIIWSA CRDLKRCPRE LPPTLLGNSS EEESQLETNV
481 TYWEEEQEFE VVSTLRLQHV DRPLSVRCTL RNAVGQDTQE VIVVPHSLPF KVVVISAILA
541 LVVLTIISLI ILIMLWQKKP RYEIRWKVIE SVSSDGHEYI YVDPMQLPYD STWELPRDQL
601 VLGRTLGSGA FGQVVEATAH GLSHSQATMK VAVKMLKSTA RSSEKQALMS ELKIMSHLGP
661 HLNVVNLLGA CTKGGPIYII TEYCRYGDLV DYLHRNKHTF LQHHSDKRRP PSAELYSNAL
721 PVGLPLPSHV SLTGESDGGY MDMSKDESVD YVPMLDMKGD VKYADIESSN YMAPYDNYVP
781 SAPERTCRAT LINESPVLSY MDLVGFSYQV ANGMEFLASK NCVHRDLAAR NVLICEGKLV
841 KICDFGLARD IMRDSNYISK GSTFLPLKWM APESIFNSLY TTLSDVWSFG ILLWEIFTLG
901 GTPYPELPMN EQFYNAIKRG YRMAQPAHAS DEIYEIMQKC WEEKFEIRPP FSQLVLLLER
961 LLGEGYKKKY QQVDEEFLRS DHPAILRSQA RLPGFHGLRS PLDTSSVLYT AVQPNEGDND
1021 YIIPLPDPKP EVADEGPLEG SPSLASSTLN EVNTSSTISC DSPLEPQDEP EPEPQLELQV
1081 EPEPELEQLP DSGCPAPRAE AEDSFLLocalizationUniProt · AlphaFold · HPA
Whether an antibody against PDGFRB can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.
- Antibody reachability
- Cell surface
- Secreted
- No
- Transmembrane segments
- 1
- Mean surface accessibility (rSASA)
- 0.37
- Highest tissue expression
- 190 nTPM
Expression across tissuesHPA
Tissue
- blood vessel: 190 nTPM
- adipose tissue: 165 nTPM
- cervix: 139 nTPM
- gallbladder: 117 nTPM
- placenta: 106 nTPM
- breast: 102 nTPM
Single-cell type
- pericytes: 780 nCPM
- vascular smooth muscle cells: 399 nCPM
- peritubular myoid cells: 294 nCPM
- leydig cells: 238 nCPM
- fibroblasts: 197 nCPM
- fibro-adipogenic progenitors: 193 nCPM
Immune cell
- non-classical monocyte: 1.6 nTPM
- gdT-cell: 0.9 nTPM
- naive CD8 T-cell: 0.3 nTPM
- intermediate monocyte: 0.2 nTPM
- memory CD8 T-cell: 0.2 nTPM
- total PBMC: 0.2 nTPM
Brain region
- choroid plexus: 68 nTPM
- cerebral cortex: 42 nTPM
- thalamus: 35 nTPM
- basal ganglia: 33 nTPM
- amygdala: 29 nTPM
- midbrain: 28 nTPM
DiseaseUniProt · ClinVar · IEDB · PubMed
Four sources answering four different questions about PDGFRB.
Disease | AllUniProt
Conditions PDGFRB is implicated in, by any mechanism.
- Myeloproliferative disorder chronic with eosinophilia (MPE) MIM:131440
- Leukemia, acute myelogenous (AML) MIM:601626
- Leukemia, juvenile myelomonocytic (JMML) MIM:607785
- Basal ganglia calcification, idiopathic, 4 (IBGC4) MIM:615007
- Myofibromatosis, infantile 1 (IMF1) MIM:228550
- Kosaki overgrowth syndrome (KOGS) MIM:616592
- Premature aging syndrome, Penttinen type (PENTT) MIM:601812
- Ocular pterygium-digital keloid dysplasia syndrome (OPDKD) MIM:621091
Disease | GeneticClinVar
28 pathogenic / likely-pathogenic of 851 ClinVar records.
Conditions with pathogenic or likely-pathogenic variants.
- Infantile myofibromatosis
- Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome
- Acroosteolysis-keloid-like lesions-premature aging syndrome
- Basal ganglia calcification, idiopathic, 4
- Myofibromatosis, infantile, 1
ReferencesPubMed · IEDB
Publications for PDGFRB from three distinct lines of evidence, kept separate because they answer different questions: whether antibodies are directed at the protein, whether a B-cell epitope has been mapped on it, and whether a T-cell epitope has. Each is labelled with its source.
Reference: AutoantibodyPubMed
2 publications
- Lack of evidence of stimulatory autoantibodies to platelet-derived growth factor receptor in patients with systemic sclerosis.
2009 · Arthritis Rheum · RCR 1.9 · 72 citations - Lack of detection of agonist activity by antibodies to platelet-derived growth factor receptor alpha in a subset of normal and systemic sclerosis patient sera.
2009 · Arthritis Rheum · RCR 1.5 · 62 citations
Reference: B cellIEDB
1 publication
- Peptide microarray-based characterization of antibody responses to host proteins after bacille Calmette-Guérin vaccination.
2017 · Int J Infect Dis · RCR 0.7 · 19 citations
Sources: PubMed — antigen-level antibody evidence from a custom retrieval. Records matching a controlled set of autoantibody terms (the MeSH descriptors Autoantibodies and Autoantigens, with title and abstract term variants) were obtained through NCBI E-utilities, and their titles and abstracts parsed for constructions that direct an antibody at a named protein rather than for co-occurrence. Captured names were resolved against UniProt nomenclature and each antigen adjudicated individually against the source text. IEDB — curated epitope assays from the Immune Epitope Database (Vita et al., Nucleic Acids Research 2019). Bibliographic records from PubMed and MeSH, U.S. National Library of Medicine; citation metrics from NIH iCite (Hutchins et al., PLoS Biology 2016). Titles link to PubMed; abstracts are not reproduced here. The NLM does not endorse this analysis.
Genetic constraint and essentialitygnomAD · DepMap
Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.
- gnomAD LOEUF (loss-of-function intolerance)
- 0.33
- gnomAD pLI
- 0.9
- gnomAD missense Z
- 1.84
- DepMap mean gene effect
- -0.16
- DepMap dependency class
- selective
Cancer expressionTCGA
Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).
OntologyGO
Biological processes
- angiogenesis
- aorta morphogenesis
- cardiac myofibril assembly
- cell chemotaxis
- cell migration involved in vasculogenesis
- cell surface receptor protein tyrosine kinase signaling pathway
- metanephric glomerular capillary formation
- peptidyl-tyrosine phosphorylation
- platelet-derived growth factor receptor signaling pathway
- platelet-derived growth factor receptor-beta signaling pathway
- positive regulation of calcium ion import
- positive regulation of calcium-mediated signaling
- positive regulation of cell migration
- positive regulation of cell population proliferation
- positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway
- positive regulation of chemotaxis
- positive regulation of DNA biosynthetic process
- positive regulation of ERK1 and ERK2 cascade
- positive regulation of MAP kinase activity
- positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway
- positive regulation of mitotic nuclear division
- positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
- positive regulation of reactive oxygen species metabolic process
- positive regulation of smooth muscle cell migration
- positive regulation of smooth muscle cell proliferation
- protein autophosphorylation
- regulation of actin cytoskeleton organization
- retina vasculature development in camera-type eye
- signal transduction
- smooth muscle adaptation
- smooth muscle cell chemotaxis
- cell migration involved in coronary angiogenesis
- metanephric glomerular mesangial cell proliferation involved in metanephros development
Molecular functions
- ATP binding
- enzyme binding
- GTPase activator activity
- phospholipase C activator activity
- platelet activating factor receptor activity
- platelet-derived growth factor beta-receptor activity
- platelet-derived growth factor binding
- platelet-derived growth factor receptor binding
- protein kinase activity
- protein kinase binding
- protein tyrosine kinase activity
- signaling receptor binding
- vascular endothelial growth factor binding
- platelet-derived growth factor receptor activity
Cellular components
Protein domainsUniProt · Pfam · InterPro
- Protein kinase domain
- Serine-threonine/tyrosine-protein kinase, catalytic domain
- Tyrosine-protein kinase, receptor class III, conserved site
- Immunoglobulin subtype 2
- Immunoglobulin domain subtype
- Immunoglobulin-like domain
- Tyrosine-protein kinase, active site
- Protein kinase-like domain superfamily
- Immunoglobulin-like beta-sandwich domain
- Immunoglobulin-like fold
- Protein kinase, ATP binding site
- Tyrosine-protein kinase, catalytic domain
- Immunoglobulin-like domain superfamily
- Receptor Tyrosine Kinase
- Immunoglobulin domain
- Protein tyrosine and serine/threonine kinase
- Immunoglobulin domain
- Platelet-derived growth factor receptor Ig-like domain 4
- Platelet-derived growth factor receptor beta
KeywordsUniProt
- ATP-binding
- Cell membrane
- Chemotaxis
- Chromosomal rearrangement
- Cytoplasmic vesicle
- Developmental protein
- Disulfide bond
- Glycoprotein
- Immunoglobulin domain
- Kinase
- Lysosome
- Membrane
- Nucleotide-binding
- Phosphoprotein
- Proto-oncogene
- Receptor
- Repeat
- Signal
- Transferase
- Transmembrane
- Transmembrane helix
- Tyrosine-protein kinase
- Ubl conjugation
InteractionsUniProt · HPA
Protein binding partners of PDGFRB in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.
Antibody and autoantibody relevanceSeroatlas analysis
Seroatlas reads PDGFRB as an antibody target. Whether an autoantibody or antibody against PDGFRB could matter depends on whether native PDGFRB is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.
PDGFRB is annotated at the cell surface, where native PDGFRB is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.
Annotation status
The present source text does not explicitly label PDGFRB as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.
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