Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Platelet-derived growth factor D

Gene

Pdgfd

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at transcript 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. Plays an important role in wound healing (By similarity). Has oncogenic potential and can induce tumor formation. Induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix.By similarity3 Publications

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein, Growth factor, Mitogen

Enzyme and pathway databases

ReactomeiR-MMU-186797 Signaling by PDGF

Names & Taxonomyi

Protein namesi
Recommended name:
Platelet-derived growth factor D
Short name:
PDGF-D
Alternative name(s):
Spinal cord-derived growth factor B
Short name:
SCDGF-B
Cleaved into the following 2 chains:
Platelet-derived growth factor D, receptor-binding form
Short name:
PDGFD receptor-binding form
Gene namesi
Name:Pdgfd
Synonyms:Scdgfb
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 9

Organism-specific databases

MGIiMGI:1919035 Pdgfd

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

Keywords - Diseasei

Proto-oncogene

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 23Sequence analysisAdd BLAST23
ChainiPRO_000025019024 – 370Platelet-derived growth factor D, latent formAdd BLAST347
ChainiPRO_0000250191250 – 370Platelet-derived growth factor D, receptor-binding formSequence analysisAdd BLAST121

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi109 ↔ 131PROSITE-ProRule annotation
Glycosylationi276N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi296InterchainPROSITE-ProRule annotation
Disulfide bondi302 ↔ 360PROSITE-ProRule annotation
Disulfide bondi306 ↔ 362PROSITE-ProRule annotation

Post-translational modificationi

Activated by proteolytic cleavage. Proteolytic removal of the N-terminal CUB domain releasing the core domain is necessary for unmasking the receptor-binding epitopes of the core domain. Cleavage after Arg-247 or Arg-249 by urokinase plasminogen activator gives rise to the active form (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei247 – 248CleavageSequence analysis2
Sitei249 – 250CleavageSequence analysis2

Keywords - PTMi

Cleavage on pair of basic residues, Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ925I7
PeptideAtlasiQ925I7
PRIDEiQ925I7

PTM databases

PhosphoSitePlusiQ925I7

Expressioni

Tissue specificityi

Expressed at high levels in developing heart, lung, kidney and some muscle derivatives. Moderately expressed in liver, brain and testis. In the kidney, localized to glomerular mesangial cells and vascular smooth muscle cells. Up-regulated in areas of renal fibrosis. In mice with unilateral ureteral obstruction, expressed in interstitial cells at day 4, with an increased to maximal expression at day 14.4 Publications

Gene expression databases

BgeeiENSMUSG00000032006 Expressed in 215 organ(s), highest expression level in aorta
CleanExiMM_PDGFD
GenevisibleiQ925I7 MM

Interactioni

Subunit structurei

Homodimer; disulfide-linked. Interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

ComplexPortaliCPX-2915 Platelet-derived growth factor DD complex
CPX-2916 PDGF receptor alpha-beta - PDGF-DD complex
CPX-2917 PDGF receptor beta - PDGF-DD complex
STRINGi10090.ENSMUSP00000128388

Structurei

3D structure databases

ProteinModelPortaliQ925I7
SMRiQ925I7
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini52 – 170CUBPROSITE-ProRule annotationAdd BLAST119

Sequence similaritiesi

Belongs to the PDGF/VEGF growth factor family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG410IGUN Eukaryota
ENOG41106HA LUCA
GeneTreeiENSGT00390000005171
HOGENOMiHOG000261610
HOVERGENiHBG057324
InParanoidiQ925I7
KOiK05450
OMAiLYRKEET
OrthoDBiEOG091G08SH
PhylomeDBiQ925I7
TreeFamiTF332130

Family and domain databases

CDDicd00041 CUB, 1 hit
cd00135 PDGF, 1 hit
Gene3Di2.10.90.10, 1 hit
2.60.120.290, 1 hit
InterProiView protein in InterPro
IPR000859 CUB_dom
IPR029034 Cystine-knot_cytokine
IPR000072 PDGF/VEGF_dom
IPR027123 PDGFD
IPR035914 Sperma_CUB_dom_sf
PANTHERiPTHR11633:SF4 PTHR11633:SF4, 1 hit
PfamiView protein in Pfam
PF00431 CUB, 1 hit
PF00341 PDGF, 1 hit
SMARTiView protein in SMART
SM00042 CUB, 1 hit
SM00141 PDGF, 1 hit
SUPFAMiSSF49854 SSF49854, 1 hit
SSF57501 SSF57501, 1 hit
PROSITEiView protein in PROSITE
PS01180 CUB, 1 hit
PS50278 PDGF_2, 1 hit

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q925I7-1) [UniParc]FASTAAdd to basket
Also known as: Long

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
MQRLVLVSIL LCANFSCYPD TFATPQRASI KALRNANLRR DESNHLTDLY
60 70 80 90 100
QREENIQVTS NGHVQSPRFP NSYPRNLLLT WWLRSQEKTR IQLSFDHQFG
110 120 130 140 150
LEEAENDICR YDFVEVEEVS ESSTVVRGRW CGHKEIPPRI TSRTNQIKIT
160 170 180 190 200
FKSDDYFVAK PGFKIYYSFV EDFQPEAASE TNWESVTSSF SGVSYHSPSI
210 220 230 240 250
TDPTLTADAL DKTVAEFDTV EDLLKHFNPV SWQDDLENLY LDTPHYRGRS
260 270 280 290 300
YHDRKSKVDL DRLNDDVKRY SCTPRNHSVN LREELKLTNA VFFPRCLLVQ
310 320 330 340 350
RCGGNCGCGT VNWKSCTCSS GKTVKKYHEV LKFEPGHFKR RGKAKNMALV
360 370
DIQLDHHERC DCICSSRPPR
Length:370
Mass (Da):42,809
Last modified:December 1, 2001 - v1
Checksum:i9E80B4CF6813BFBE
GO
Isoform 2 (identifier: Q925I7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     42-47: Missing.

Show »
Length:364
Mass (Da):42,127
Checksum:i4273B8715A7DBC97
GO
Isoform 3 (identifier: Q925I7-3) [UniParc]FASTAAdd to basket
Also known as: Short

The sequence of this isoform differs from the canonical sequence as follows:
     258-261: VDLD → GIEV
     262-370: Missing.

Show »
Length:261
Mass (Da):30,289
Checksum:i3AA92B3236B16809
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti173F → S in AAH30896 (PubMed:15489334).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_02061642 – 47Missing in isoform 2. 1 Publication6
Alternative sequenceiVSP_020617258 – 261VDLD → GIEV in isoform 3. 2 Publications4
Alternative sequenceiVSP_020618262 – 370Missing in isoform 3. 2 PublicationsAdd BLAST109

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF335583 mRNA Translation: AAK38839.1
AK003359 mRNA Translation: BAB22735.2
AK141551 mRNA Translation: BAE24732.1
BC030896 mRNA Translation: AAH30896.1
CCDSiCCDS22801.1 [Q925I7-1]
RefSeqiNP_082200.1, NM_027924.2 [Q925I7-1]
XP_006509948.1, XM_006509885.3
XP_006509949.1, XM_006509886.3
UniGeneiMm.390122

Genome annotation databases

EnsembliENSMUST00000058692; ENSMUSP00000056240; ENSMUSG00000032006 [Q925I7-2]
ENSMUST00000168039; ENSMUSP00000128388; ENSMUSG00000032006 [Q925I7-1]
ENSMUST00000214892; ENSMUSP00000149162; ENSMUSG00000032006 [Q925I7-3]
GeneIDi71785
KEGGimmu:71785
UCSCiuc009oby.1 mouse [Q925I7-1]
uc009obz.1 mouse [Q925I7-2]
uc012gnq.1 mouse [Q925I7-3]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF335583 mRNA Translation: AAK38839.1
AK003359 mRNA Translation: BAB22735.2
AK141551 mRNA Translation: BAE24732.1
BC030896 mRNA Translation: AAH30896.1
CCDSiCCDS22801.1 [Q925I7-1]
RefSeqiNP_082200.1, NM_027924.2 [Q925I7-1]
XP_006509948.1, XM_006509885.3
XP_006509949.1, XM_006509886.3
UniGeneiMm.390122

3D structure databases

ProteinModelPortaliQ925I7
SMRiQ925I7
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

ComplexPortaliCPX-2915 Platelet-derived growth factor DD complex
CPX-2916 PDGF receptor alpha-beta - PDGF-DD complex
CPX-2917 PDGF receptor beta - PDGF-DD complex
STRINGi10090.ENSMUSP00000128388

PTM databases

PhosphoSitePlusiQ925I7

Proteomic databases

PaxDbiQ925I7
PeptideAtlasiQ925I7
PRIDEiQ925I7

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000058692; ENSMUSP00000056240; ENSMUSG00000032006 [Q925I7-2]
ENSMUST00000168039; ENSMUSP00000128388; ENSMUSG00000032006 [Q925I7-1]
ENSMUST00000214892; ENSMUSP00000149162; ENSMUSG00000032006 [Q925I7-3]
GeneIDi71785
KEGGimmu:71785
UCSCiuc009oby.1 mouse [Q925I7-1]
uc009obz.1 mouse [Q925I7-2]
uc012gnq.1 mouse [Q925I7-3]

Organism-specific databases

CTDi80310
MGIiMGI:1919035 Pdgfd

Phylogenomic databases

eggNOGiENOG410IGUN Eukaryota
ENOG41106HA LUCA
GeneTreeiENSGT00390000005171
HOGENOMiHOG000261610
HOVERGENiHBG057324
InParanoidiQ925I7
KOiK05450
OMAiLYRKEET
OrthoDBiEOG091G08SH
PhylomeDBiQ925I7
TreeFamiTF332130

Enzyme and pathway databases

ReactomeiR-MMU-186797 Signaling by PDGF

Miscellaneous databases

PROiPR:Q925I7
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000032006 Expressed in 215 organ(s), highest expression level in aorta
CleanExiMM_PDGFD
GenevisibleiQ925I7 MM

Family and domain databases

CDDicd00041 CUB, 1 hit
cd00135 PDGF, 1 hit
Gene3Di2.10.90.10, 1 hit
2.60.120.290, 1 hit
InterProiView protein in InterPro
IPR000859 CUB_dom
IPR029034 Cystine-knot_cytokine
IPR000072 PDGF/VEGF_dom
IPR027123 PDGFD
IPR035914 Sperma_CUB_dom_sf
PANTHERiPTHR11633:SF4 PTHR11633:SF4, 1 hit
PfamiView protein in Pfam
PF00431 CUB, 1 hit
PF00341 PDGF, 1 hit
SMARTiView protein in SMART
SM00042 CUB, 1 hit
SM00141 PDGF, 1 hit
SUPFAMiSSF49854 SSF49854, 1 hit
SSF57501 SSF57501, 1 hit
PROSITEiView protein in PROSITE
PS01180 CUB, 1 hit
PS50278 PDGF_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPDGFD_MOUSE
AccessioniPrimary (citable) accession number: Q925I7
Secondary accession number(s): Q3URF6, Q8K2L3, Q9D1L8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: December 1, 2001
Last modified: November 7, 2018
This is version 123 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again