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PDGFRB
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  • PDGFRB
PROTEIN STRUCTURE
ANTIBODIES
AND
VALIDATION
Protein structures
GENERAL INFORMATIONi

General description of the gene and the encoded protein(s) using information from HGNC and Ensembl, as well as predictions made by the Human Protein Atlas project.

Gene namei

Official gene symbol, which is typically a short form of the gene name, according to HGNC.

PDGFRB
Synonyms CD140b, JTK12, PDGFR, PDGFR1
Gene descriptioni

Full gene name according to HGNC.

Platelet derived growth factor receptor beta
Protein classi

Assigned HPA protein class(es) for the encoded protein(s).

Read more
Cancer-related genes
CD markers
Disease related genes
Enzymes
FDA approved drug targets
Human disease related genes
Plasma proteins
RAS pathway related proteins
Predicted locationi

All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions.

  • Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached.

  • Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s).

The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.

Read more
Intracellular,Membrane
Protein evidence Evidence at protein level (all genes)
GENE INFORMATIONi

Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.

Chromosome 5
Cytoband q32
Chromosome location (bp) 150113839 - 150155872
Number of transcriptsi

Number of protein-coding transcripts from the gene as defined by Ensembl.

3
Ensembl ENSG00000113721 (version 103.38)
Entrez gene 5159
HGNC HGNC:8804
UniProt P09619 (UniProt - Evidence at protein level)
neXtProt NX_P09619
Antibodypedia PDGFRB antibodies


PROTEIN STRUCTUREi

The Structure section provides predicted structures from the Alphafold protein structure database and available experimental structures from Protein Data Bank (PDB).

In the Structure drop-down menu all experimental structures from PDB are available for selection and display. The structures are displayed using the NGL Viewer and can be zoomed-in and rotated either manually or by checking the Autorotate box. The Color scheme can be selected to show the residue index, chain name or confidence score (as B-factors and pLDDT score for experimental and predicted structures, respectively). The positions for available antigen sequences in the structure are shown if Antigens is turned to ON, and the Variants slider can be used to show the positions of clinical and population variants.https://github.com/nglviewer/ngl

Read more

Predicted


Description: Structure prediction from Alphafold project. Structure version 2

# Chains: 1      # Clinical variants: 11      # Population variants: 645

Antigens:

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On

Variants:

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Clinical
Population

Color scheme:

Confidence
Residue index
Chain name

Autorotate:

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On



PROTEIN BROWSERi

The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.

At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.

Below the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more).

The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more).

If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.

Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.
PDGFRB-201
PDGFRB-202
PDGFRB-204


PROTEIN INFORMATIONi

The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.

The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.

The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.

The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.
Splice variant UniProt Protein class Gene ontology Length & mass Signal peptide
(predicted)
Transmembrane regions
(predicted)
PDGFRB-201
ENSP00000261799
ENST00000261799
P09619 [Direct mapping]
Platelet-derived growth factor receptor beta
Show all
Enzymes
   ENZYME proteins
   Transferases
   Kinases
   Tyr protein kinases
CD markers
Predicted membrane proteins
   Prediction method-based
   Membrane proteins predicted by MDM
   MEMSAT3 predicted membrane proteins
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   SCAMPI predicted membrane proteins
   SPOCTOPUS predicted membrane proteins
   THUMBUP predicted membrane proteins
   TMHMM predicted membrane proteins
   # TM segments-based
   1TM proteins predicted by MDM
Plasma proteins
RAS pathway related proteins
Cancer-related genes
   Candidate cancer biomarkers
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Translocations
Disease related genes
FDA approved drug targets
   Biotech drugs
   Small molecule drugs
Human disease related genes
   Cancers
   Cancers of eye, brain, and central nervous system
   Nervous system diseases
   Neurodegenerative diseases
   Skin diseases
   Skin and soft tissue diseases
Mapped to neXtProt
   neXtProt - Evidence at protein level
Protein evidence (Kim et al 2014)
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0000165 [MAPK cascade]
GO:0000166 [nucleotide binding]
GO:0004672 [protein kinase activity]
GO:0004713 [protein tyrosine kinase activity]
GO:0004714 [transmembrane receptor protein tyrosine kinase activity]
GO:0004992 [platelet activating factor receptor activity]
GO:0005017 [platelet-derived growth factor-activated receptor activity]
GO:0005019 [platelet-derived growth factor beta-receptor activity]
GO:0005102 [signaling receptor binding]
GO:0005161 [platelet-derived growth factor receptor binding]
GO:0005515 [protein binding]
GO:0005524 [ATP binding]
GO:0005634 [nucleus]
GO:0005737 [cytoplasm]
GO:0005764 [lysosome]
GO:0005794 [Golgi apparatus]
GO:0005886 [plasma membrane]
GO:0005887 [integral component of plasma membrane]
GO:0005925 [focal adhesion]
GO:0006024 [glycosaminoglycan biosynthetic process]
GO:0006468 [protein phosphorylation]
GO:0006935 [chemotaxis]
GO:0007165 [signal transduction]
GO:0007169 [transmembrane receptor protein tyrosine kinase signaling pathway]
GO:0007186 [G protein-coupled receptor signaling pathway]
GO:0007275 [multicellular organism development]
GO:0007568 [aging]
GO:0008284 [positive regulation of cell population proliferation]
GO:0008584 [male gonad development]
GO:0009636 [response to toxic substance]
GO:0009986 [cell surface]
GO:0010863 [positive regulation of phospholipase C activity]
GO:0014068 [positive regulation of phosphatidylinositol 3-kinase signaling]
GO:0014070 [response to organic cyclic compound]
GO:0014911 [positive regulation of smooth muscle cell migration]
GO:0016020 [membrane]
GO:0016021 [integral component of membrane]
GO:0016301 [kinase activity]
GO:0016310 [phosphorylation]
GO:0016324 [apical plasma membrane]
GO:0016477 [cell migration]
GO:0016740 [transferase activity]
GO:0018108 [peptidyl-tyrosine phosphorylation]
GO:0019838 [growth factor binding]
GO:0019899 [enzyme binding]
GO:0019901 [protein kinase binding]
GO:0030335 [positive regulation of cell migration]
GO:0031226 [intrinsic component of plasma membrane]
GO:0031410 [cytoplasmic vesicle]
GO:0032355 [response to estradiol]
GO:0032516 [positive regulation of phosphoprotein phosphatase activity]
GO:0032526 [response to retinoic acid]
GO:0032956 [regulation of actin cytoskeleton organization]
GO:0032967 [positive regulation of collagen biosynthetic process]
GO:0033674 [positive regulation of kinase activity]
GO:0033993 [response to lipid]
GO:0034405 [response to fluid shear stress]
GO:0035025 [positive regulation of Rho protein signal transduction]
GO:0035441 [cell migration involved in vasculogenesis]
GO:0035556 [intracellular signal transduction]
GO:0035789 [metanephric mesenchymal cell migration]
GO:0035791 [platelet-derived growth factor receptor-beta signaling pathway]
GO:0035793 [positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway]
GO:0035909 [aorta morphogenesis]
GO:0036120 [cellular response to platelet-derived growth factor stimulus]
GO:0038085 [vascular endothelial growth factor binding]
GO:0038091 [positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway]
GO:0042060 [wound healing]
GO:0042542 [response to hydrogen peroxide]
GO:0043065 [positive regulation of apoptotic process]
GO:0043066 [negative regulation of apoptotic process]
GO:0043202 [lysosomal lumen]
GO:0043231 [intracellular membrane-bounded organelle]
GO:0043235 [receptor complex]
GO:0043406 [positive regulation of MAP kinase activity]
GO:0043548 [phosphatidylinositol 3-kinase binding]
GO:0043552 [positive regulation of phosphatidylinositol 3-kinase activity]
GO:0043627 [response to estrogen]
GO:0045840 [positive regulation of mitotic nuclear division]
GO:0046488 [phosphatidylinositol metabolic process]
GO:0046777 [protein autophosphorylation]
GO:0048008 [platelet-derived growth factor receptor signaling pathway]
GO:0048015 [phosphatidylinositol-mediated signaling]
GO:0048146 [positive regulation of fibroblast proliferation]
GO:0048407 [platelet-derived growth factor binding]
GO:0048661 [positive regulation of smooth muscle cell proliferation]
GO:0048839 [inner ear development]
GO:0050921 [positive regulation of chemotaxis]
GO:0051897 [positive regulation of protein kinase B signaling]
GO:0055003 [cardiac myofibril assembly]
GO:0055093 [response to hyperoxia]
GO:0060326 [cell chemotaxis]
GO:0060437 [lung growth]
GO:0060981 [cell migration involved in coronary angiogenesis]
GO:0061298 [retina vasculature development in camera-type eye]
GO:0070374 [positive regulation of ERK1 and ERK2 cascade]
GO:0071670 [smooth muscle cell chemotaxis]
GO:0072075 [metanephric mesenchyme development]
GO:0072262 [metanephric glomerular mesangial cell proliferation involved in metanephros development]
GO:0072275 [metanephric glomerulus morphogenesis]
GO:0072277 [metanephric glomerular capillary formation]
GO:0072278 [metanephric comma-shaped body morphogenesis]
GO:0072284 [metanephric S-shaped body morphogenesis]
GO:0090280 [positive regulation of calcium ion import]
GO:2000379 [positive regulation of reactive oxygen species metabolic process]
GO:2000491 [positive regulation of hepatic stellate cell activation]
GO:2000573 [positive regulation of DNA biosynthetic process]
Show all
1106 aa
124 kDa
Yes 1
PDGFRB-202
ENSP00000429218
ENST00000517488
E5RJ14 [Direct mapping]
Platelet-derived growth factor receptor beta
Show all
Predicted intracellular proteins
   Intracellular proteins predicted by MDM and MDSEC
RAS pathway related proteins
Cancer-related genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Translocations
Human disease related genes
   Cancers
   Cancers of eye, brain, and central nervous system
   Nervous system diseases
   Neurodegenerative diseases
   Skin diseases
   Skin and soft tissue diseases
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005794 [Golgi apparatus]
GO:0043231 [intracellular membrane-bounded organelle]
Show all
146 aa
16.6 kDa
No 0
PDGFRB-204
ENSP00000430715
ENST00000517957
E5RII0 [Direct mapping]
Platelet-derived growth factor receptor beta
Show all
   MEMSAT-SVM predicted membrane proteins
   Phobius predicted membrane proteins
   Secreted proteins predicted by MDSEC
   SignalP predicted secreted proteins
   Phobius predicted secreted proteins
   SPOCTOPUS predicted secreted proteins
Predicted intracellular proteins
RAS pathway related proteins
Cancer-related genes
   COSMIC somatic mutations in cancer genes
   COSMIC Somatic Mutations
   COSMIC Translocations
Human disease related genes
   Cancers
   Cancers of eye, brain, and central nervous system
   Nervous system diseases
   Neurodegenerative diseases
   Skin diseases
   Skin and soft tissue diseases
Protein evidence (Ezkurdia et al 2014)
Show all
GO:0005794 [Golgi apparatus]
GO:0043231 [intracellular membrane-bounded organelle]
Show all
174 aa
19.1 kDa
Yes 0

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The Human Protein Atlas project is funded
by the Knut & Alice Wallenberg Foundation.