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Protein

Platelet-derived growth factor subunit B

Gene

PDGFB

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

Functioni

Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin (PubMed:26599395). Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).By similarity1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei108Involved in receptor binding1
Sitei111Involved in receptor binding1

GO - Molecular functioni

  • chemoattractant activity Source: BHF-UCL
  • collagen binding Source: MGI
  • growth factor activity Source: UniProtKB
  • identical protein binding Source: IntAct
  • phosphatidylinositol-4,5-bisphosphate 3-kinase activity Source: Reactome
  • platelet-derived growth factor binding Source: BHF-UCL
  • platelet-derived growth factor receptor binding Source: BHF-UCL
  • protein heterodimerization activity Source: BHF-UCL
  • protein homodimerization activity Source: BHF-UCL
  • Ras guanyl-nucleotide exchange factor activity Source: Reactome
  • superoxide-generating NADPH oxidase activator activity Source: UniProtKB

GO - Biological processi

  • activation of protein kinase activity Source: UniProtKB
  • activation of protein kinase B activity Source: UniProtKB
  • cell chemotaxis Source: UniProtKB
  • cellular response to growth factor stimulus Source: BHF-UCL
  • cellular response to mycophenolic acid Source: UniProtKB
  • embryonic placenta development Source: UniProtKB
  • extracellular matrix organization Source: Reactome
  • heart development Source: UniProtKB
  • interleukin-18-mediated signaling pathway Source: BHF-UCL
  • MAPK cascade Source: Reactome
  • metanephric glomerular mesangial cell development Source: UniProtKB
  • monocyte chemotaxis Source: BHF-UCL
  • negative regulation of gene expression Source: BHF-UCL
  • negative regulation of phosphatidylinositol biosynthetic process Source: BHF-UCL
  • negative regulation of platelet activation Source: BHF-UCL
  • negative regulation of pri-miRNA transcription by RNA polymerase II Source: BHF-UCL
  • negative regulation of protein binding Source: UniProtKB
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • negative regulation of vascular smooth muscle cell differentiation Source: BHF-UCL
  • paracrine signaling Source: UniProtKB
  • peptidyl-serine phosphorylation Source: UniProtKB
  • peptidyl-tyrosine phosphorylation Source: UniProtKB
  • platelet degranulation Source: Reactome
  • platelet-derived growth factor receptor signaling pathway Source: BHF-UCL
  • positive regulation of blood vessel endothelial cell migration Source: BHF-UCL
  • positive regulation of calcium ion import Source: UniProtKB
  • positive regulation of cell division Source: UniProtKB-KW
  • positive regulation of cell migration Source: UniProtKB
  • positive regulation of cell proliferation Source: BHF-UCL
  • positive regulation of chemotaxis Source: UniProtKB
  • positive regulation of cyclin-dependent protein serine/threonine kinase activity Source: UniProtKB
  • positive regulation of DNA biosynthetic process Source: UniProtKB
  • positive regulation of endothelial cell proliferation Source: BHF-UCL
  • positive regulation of ERK1 and ERK2 cascade Source: UniProtKB
  • positive regulation of fibroblast proliferation Source: UniProtKB
  • positive regulation of gene expression Source: UniProtKB
  • positive regulation of glomerular filtration Source: UniProtKB
  • positive regulation of glomerular mesangial cell proliferation Source: UniProtKB
  • positive regulation of hyaluronan biosynthetic process Source: UniProtKB
  • positive regulation of MAPK cascade Source: UniProtKB
  • positive regulation of MAP kinase activity Source: UniProtKB
  • positive regulation of metanephric mesenchymal cell migration Source: UniProtKB
  • positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway Source: UniProtKB
  • positive regulation of mitotic nuclear division Source: UniProtKB
  • positive regulation of peptidyl-tyrosine phosphorylation Source: BHF-UCL
  • positive regulation of phosphatidylinositol 3-kinase activity Source: UniProtKB
  • positive regulation of phosphatidylinositol 3-kinase signaling Source: UniProtKB
  • positive regulation of pri-miRNA transcription by RNA polymerase II Source: BHF-UCL
  • positive regulation of protein autophosphorylation Source: UniProtKB
  • positive regulation of protein kinase B signaling Source: Reactome
  • positive regulation of protein tyrosine kinase activity Source: UniProtKB
  • positive regulation of reactive oxygen species metabolic process Source: UniProtKB
  • positive regulation of smooth muscle cell migration Source: BHF-UCL
  • positive regulation of smooth muscle cell proliferation Source: BHF-UCL
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of vascular associated smooth muscle cell migration Source: UniProtKB
  • positive regulation of vascular smooth muscle cell dedifferentiation Source: BHF-UCL
  • positive regulation of vascular smooth muscle cell proliferation Source: UniProtKB
  • protein kinase C signaling Source: UniProtKB
  • protein phosphorylation Source: UniProtKB
  • reactive oxygen species metabolic process Source: UniProtKB
  • response to wounding Source: BHF-UCL

Keywordsi

Molecular functionDevelopmental protein, Growth factor, Mitogen

Enzyme and pathway databases

ReactomeiR-HSA-114608 Platelet degranulation
R-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-3000171 Non-integrin membrane-ECM interactions
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-6811558 PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
SignaLinkiP01127
SIGNORiP01127

Names & Taxonomyi

Protein namesi
Recommended name:
Platelet-derived growth factor subunit B
Short name:
PDGF subunit B
Alternative name(s):
PDGF-2
Platelet-derived growth factor B chain
Platelet-derived growth factor beta polypeptide
Proto-oncogene c-Sis
INN: Becaplermin
Gene namesi
Name:PDGFB
Synonyms:PDGF2, SIS
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

EuPathDBiHostDB:ENSG00000100311.16
HGNCiHGNC:8800 PDGFB
MIMi190040 gene
neXtProtiNX_P01127

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Involvement in diseasei

Basal ganglia calcification, idiopathic, 5 (IBGC5)2 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:615483
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0708709L → R in IBGC5; loss of protein expression. 2 Publications1
Natural variantiVAR_070871119L → P in IBGC5; loss of protein expression. 2 PublicationsCorresponds to variant dbSNP:rs397515632EnsemblClinVar.1
A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.1 Publication

Pharmaceutical usei

Available under the name Regranex (Ortho-McNeil). Used to promote healing in diabetic neuropathic foot ulcers.

Keywords - Diseasei

Disease mutation, Proto-oncogene

Organism-specific databases

DisGeNETi5155
MalaCardsiPDGFB
MIMi607907 phenotype
615483 phenotype
OpenTargetsiENSG00000100311
Orphaneti1980 Bilateral striopallidodentate calcinosis
31112 Dermatofibrosarcoma protuberans
263662 Familial multiple meningioma
PharmGKBiPA33145

Chemistry databases

ChEMBLiCHEMBL3108633

Polymorphism and mutation databases

BioMutaiPDGFB
DMDMi129724

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 20Add BLAST20
PropeptideiPRO_000002337121 – 81Removed in mature formAdd BLAST61
ChainiPRO_000002337282 – 190Platelet-derived growth factor subunit BAdd BLAST109
PropeptideiPRO_0000023373191 – 241Removed in mature formAdd BLAST51

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi63N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi97 ↔ 1411 Publication
Disulfide bondi124Interchain1 Publication
Disulfide bondi130 ↔ 1781 Publication
Disulfide bondi133Interchain1 Publication
Disulfide bondi134 ↔ 1801 Publication

Keywords - PTMi

Cleavage on pair of basic residues, Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiP01127
PeptideAtlasiP01127
PRIDEiP01127
ProteomicsDBi12691
51325
TopDownProteomicsiP01127-2 [P01127-2]

PTM databases

GlyConnecti754
iPTMnetiP01127
PhosphoSitePlusiP01127
UniCarbKBiP01127

Miscellaneous databases

PMAP-CutDBiP01127

Expressioni

Tissue specificityi

Expressed at high levels in the heart, brain (sustantia nigra), placenta and fetal kidney. Expressed at moderate levels in the brain (hippocampus), skeletal muscle, kidney and lung.1 Publication

Gene expression databases

BgeeiENSG00000100311
CleanExiHS_PDGFB
ExpressionAtlasiP01127 baseline and differential
GenevisibleiP01127 HS

Organism-specific databases

HPAiCAB011604
CAB018341
HPA011972

Interactioni

Subunit structurei

Homodimer; antiparallel disulfide-linked dimer. Heterodimer with PDGFA; antiparallel disulfide-linked dimer. The PDGFB homodimer interacts with PDGFRA and PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB. The heterodimer composed of PDGFA and PDGFB interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB. Interacts with XLKD1 (By similarity).By similarity

Binary interactionsi

Show more details

GO - Molecular functioni

  • chemoattractant activity Source: BHF-UCL
  • growth factor activity Source: UniProtKB
  • identical protein binding Source: IntAct
  • platelet-derived growth factor binding Source: BHF-UCL
  • platelet-derived growth factor receptor binding Source: BHF-UCL
  • protein heterodimerization activity Source: BHF-UCL
  • protein homodimerization activity Source: BHF-UCL
  • Ras guanyl-nucleotide exchange factor activity Source: Reactome

Protein-protein interaction databases

BioGridi111181, 91 interactors
ComplexPortaliCPX-1875 Platelet-derived growth factor AB complex
CPX-1876 Platelet-derived growth factor BB complex
CPX-2882 PDGF receptor beta - PDGF-BB complex
CPX-2883 PDGF receptor alpha-beta - PDGF-BB complex
CPX-2884 PDGF receptor alpha - PDGF-BB complex
CPX-2885 PDGF receptor alpha - PDGF-AB complex
CPX-2886 PDGF receptor beta - PDGF-AB complex
CPX-2892 PDGF receptor alpha-beta - PDGF-AB complex
CORUMiP01127
DIPiDIP-5737N
IntActiP01127, 7 interactors
STRINGi9606.ENSP00000330382

Chemistry databases

BindingDBiP01127

Structurei

Secondary structure

1241
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi97 – 105Combined sources9
Helixi108 – 111Combined sources4
Beta strandi118 – 121Combined sources4
Beta strandi123 – 131Combined sources9
Beta strandi140 – 159Combined sources20
Beta strandi162 – 181Combined sources20

3D structure databases

ProteinModelPortaliP01127
SMRiP01127
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP01127

Family & Domainsi

Sequence similaritiesi

Belongs to the PDGF/VEGF growth factor family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410IJ45 Eukaryota
ENOG410XWTB LUCA
GeneTreeiENSGT00510000046755
HOGENOMiHOG000286027
HOVERGENiHBG053546
InParanoidiP01127
KOiK17386
OMAiQGDPIPE
OrthoDBiEOG091G0LNU
PhylomeDBiP01127
TreeFamiTF319554

Family and domain databases

CDDicd00135 PDGF, 1 hit
Gene3Di2.10.90.10, 1 hit
InterProiView protein in InterPro
IPR029034 Cystine-knot_cytokine
IPR023581 PD_growth_factor_CS
IPR000072 PDGF/VEGF_dom
IPR006782 PDGF_N
IPR015583 PDGF_suB
PANTHERiPTHR11633:SF2 PTHR11633:SF2, 1 hit
PfamiView protein in Pfam
PF00341 PDGF, 1 hit
PF04692 PDGF_N, 1 hit
SMARTiView protein in SMART
SM00141 PDGF, 1 hit
SUPFAMiSSF57501 SSF57501, 1 hit
PROSITEiView protein in PROSITE
PS00249 PDGF_1, 1 hit
PS50278 PDGF_2, 1 hit

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 promoter usage. AlignAdd to basket

Isoform 1 (identifier: P01127-1) [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.

« Hide

        10         20         30         40         50
MNRCWALFLS LCCYLRLVSA EGDPIPEELY EMLSDHSIRS FDDLQRLLHG
60 70 80 90 100
DPGEEDGAEL DLNMTRSHSG GELESLARGR RSLGSLTIAE PAMIAECKTR
110 120 130 140 150
TEVFEISRRL IDRTNANFLV WPPCVEVQRC SGCCNNRNVQ CRPTQVQLRP
160 170 180 190 200
VQVRKIEIVR KKPIFKKATV TLEDHLACKC ETVAAARPVT RSPGGSQEQR
210 220 230 240
AKTPQTRVTI RTVRVRRPPK GKHRKFKHTH DKTALKETLG A
Length:241
Mass (Da):27,283
Last modified:July 21, 1986 - v1
Checksum:i9F9A3474CE203C0B
GO
Isoform 2 (identifier: P01127-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-21: MNRCWALFLSLCCYLRLVSAE → MFIMGL

Show »
Length:226
Mass (Da):25,502
Checksum:i523AC7394E29C0D5
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti101T → E AA sequence (PubMed:6844921).Curated1
Sequence conflicti105E → C AA sequence (PubMed:6844921).Curated1
Sequence conflicti107S → C AA sequence (PubMed:6844921).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0708709L → R in IBGC5; loss of protein expression. 2 Publications1
Natural variantiVAR_01457888I → V. Corresponds to variant dbSNP:rs17565Ensembl.1
Natural variantiVAR_070871119L → P in IBGC5; loss of protein expression. 2 PublicationsCorresponds to variant dbSNP:rs397515632EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0449131 – 21MNRCW…LVSAE → MFIMGL in isoform 2. 1 PublicationAdd BLAST21

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K01401
, K01918, J00121, K01398, K01399, K01400 Genomic DNA Translation: AAA60552.1
X02811 mRNA Translation: CAA26579.1
X02744 mRNA Translation: CAA26524.1
M12783 mRNA Translation: AAA60553.1
CR456538 mRNA Translation: CAG30424.1
Z81010 Genomic DNA No translation available.
CR541807 mRNA Translation: CAG46606.1
CH471095 Genomic DNA Translation: EAW60306.1
CH471095 Genomic DNA Translation: EAW60307.1
BC029822 mRNA Translation: AAH29822.1
BC077725 mRNA Translation: AAH77725.1
X83705 mRNA Translation: CAA58679.1
X98706 Genomic DNA Translation: CAA67262.1
K01917
, K01913, K01914, K01915, K01916 Genomic DNA Translation: AAA98793.1
X03702 mRNA Translation: CAA27333.1
X00561 Genomic DNA Translation: CAA25228.1
X00561 Genomic DNA Translation: CAA25229.1
CCDSiCCDS13987.1 [P01127-1]
CCDS33650.1 [P01127-2]
PIRiA94276 PFHUG2
RefSeqiNP_002599.1, NM_002608.3 [P01127-1]
NP_148937.1, NM_033016.3 [P01127-2]
UniGeneiHs.1976

Genome annotation databases

EnsembliENST00000331163; ENSP00000330382; ENSG00000100311 [P01127-1]
ENST00000381551; ENSP00000370963; ENSG00000100311 [P01127-2]
GeneIDi5155
KEGGihsa:5155
UCSCiuc003axe.4 human [P01127-1]

Keywords - Coding sequence diversityi

Alternative promoter usage, Chromosomal rearrangement, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiPDGFB_HUMAN
AccessioniPrimary (citable) accession number: P01127
Secondary accession number(s): G3XAG8
, P78431, Q15354, Q6FHE7, Q9UF23
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: July 18, 2018
This is version 220 of the entry and version 1 of the sequence. See 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, Pharmaceutical, Reference proteome

Documents

  1. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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