Summary: PDGF/VEGF domain

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Wikipedia: Platelet-derived growth factor
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Platelet-derived growth factor Edit Wikipedia article

"PDGF" redirects here. For the space hardware, see Power Data Grapple Fixture.

Platelet-derived growth factor (PDGF)

Identifiers

Symbol

PDGF

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

In molecular biology, platelet-derived growth factor (PDGF) is one of the numerous growth factors, or proteins that regulate cell growth and division. In particular, it plays a significant role in blood vessel formation (angiogenesis), the growth of blood vessels from already-existing blood vessel tissue. Uncontrolled angiogenesis is a characteristic of cancer. In chemical terms, platelet-derived growth factor is dimeric glycoprotein composed of two A (-AA) or two B (-BB) chains or a combination of the two (-AB).

PDGF^[1]^[2] is a potent mitogen for cells of mesenchymal origin, including smooth muscle cells and glial cells. In both mouse and human, the PDGF signalling network consists of four ligands, PDGFA-D, and two receptors, PDGFRalpha and PDGFRbeta. All PDGFs function as secreted, disulphide-linked homodimers, but only PDGFA and B can form functional heterodimers.

Though it is synthesized^[3] stored and released by platelets upon activation, it is produced by a plethora of cells including smooth muscle cells, activated macrophages, and endothelial cells^[4]

[edit] Types/Classification

There are five different isoforms of PDGF that activate cellular response through two different receptors. Known ligands include A (PDGFA), B (PDGFB), C (PDGFC), and D (PDGFD), and an AB heterodimer and receptors alpha (PDGFRA) and beta (PDGFRB). PDGF has few other members of the family, for example VEGF sub-family.

[edit] Mechanisms

The receptor for PDGF, PDGFR is classified as a receptor tyrosine kinase (RTK), a type of cell surface receptor. Two types of PDGFRs have been identified: alpha-type and beta-type PDGFRs.^[5] The alpha type binds to PDGF-AA, PDGF-BB and PDGF-AB, whereas the beta type PDGFR binds with high affinity to PDGF-BB and PDGF-AB.^[6] PDGF binds to PDGFRs ligand binding pocket located within the second and third immunoglobulin domains.^[7] Upon activation by PDGF, these receptors dimerise, and are "switched on" by auto-phosphorylation of several sites on their cytosolic domains, which serve to mediate binding of cofactors and subsequently activate signal transduction, for example, through the PI3K pathway. Downstream effects of this include regulation of gene expression and the cell cycle. The role of PI3K has been investigated by several laboratories. Accumulating data suggests that, while this molecule is, in general, part of growth signaling complex, it plays a more profound role in controlling cell migration.^[8] The different ligand isoforms have variable affinities for the receptor isoforms, and the receptor isoforms may variably form hetero- or homo- dimers. This leads to specificity of downstream signaling. It has been shown that the cis oncogene is derived from the PDGF B-chain gene. PDGF-BB is the highest-affinity ligand for the PDGFR-beta; PDGFR-beta is a key marker of hepatic stellate cell activation in the process of fibrogenesis.^{[citation needed]}

[edit] Function

PDGFs are mitogenic during early developmental stages, driving the proliferation of undifferentiated mesenchyme and some progenitor populations. During later maturation stages, PDGF signalling has been implicated in tissue remodelling and cellular differentiation, and in inductive events involved in patterning and morphogenesis. In addition to driving mesenchymal proliferation, PDGFs have been shown to direct the migration, differentiation and function of a variety of specialised mesenchymal and migratory cell types, both during development and in the adult animal.^[9] Other growth factors in this family include vascular endothelial growth factors B and C (VEGF-B, VEGF-C)^[10]^[11] which are active in angiogenesis and endothelial cell growth, and placenta growth factor (PlGF) which is also active in angiogenesis.^[12]

PDGF plays a role in embryonic development, cell proliferation, cell migration, and angiogenesis.^[13] PDGF has also been linked to several diseases such as atherosclerosis, fibrosis and malignant diseases.^{[citation needed]}

In addition, PDGF is a required element in cellular division for fibroblast, a type of connective tissue cell.^{[citation needed]} In essence, the PDGFs allow a cell to skip the G1 checkpoints in order to divide.^{[citation needed]}

PDGF is also known to maintain proliferation of oligodendrocyte progenitor cells.^{[citation needed]} ^[14]^[15]

[edit] History

PDGF was one of the first growth factors characterized,^[16] and has led to an understanding of the mechanism of many growth factor signaling pathways.^{[citation needed]}

[edit] Clinical significance

Like many other growth factors that have been linked to disease, PDGF and its receptors have provided a market for receptor antagonists to treat disease. Such antagonists include (but are not limited to) specific antibodies that target the molecule of interest, which act only in a neutralizing manner.^[17]

The "c-Sis" oncogene is derived from PDGF.^[15]^[18]

Age related downregulation of the PDGF receptor on islet beta cells has been demonstrated to prevent islet beta cell proliferation in both animal and human cells and its re-expression triggered beta cell proliferation and corrected glucose regulation via insulin secretion.^[19]^[20]

[edit] Family members

Human genes encoding proteins that belong to the platelet-derived growth factor family include:

[edit] See also

Platelet-activating factor
Platelet-derived growth factor receptor
atheroma platelet involvement in smooth muscle proliferation

[edit] References

^ Hannink M, Donoghue DJ (1989). "Structure and function of platelet-derived growth factor (PDGF) and related proteins". Biochim. Biophys. Acta 989 (1): 1â10. PMID 2546599.
^ Heldin CH (1992). "Structural and functional studies on platelet-derived growth factor". EMBO J. 11 (12): 4251â4259. PMC 556997. PMID 1425569. //www.ncbi.nlm.nih.gov/pmc/articles/PMC556997/.
^ Minarcik, John. "Global Path Course: Video". http://www.gopathdx.com/?action-model-name-lectures-itemid-69. Retrieved 2011-06-27.
^ Kumar, Vinay (2010). Robbins and Coltran Pathologic Basis of Disease. China: Elsevier. pp. 88â89. ISBN 978-1-4160-3121-5.
^ Matsui T, Heidaran M, Miki T, et al. (1989). "Isolation of a novel receptor cDNA establishes the existence of two PDGF receptor genes". Science 243 (4892): 800â4. doi:10.1126/science.2536956. PMID 2536956.
^ Heidaran MA, Pierce JH, Yu JC, et al. (25 October 1991). "Role of alpha beta receptor heterodimer formation in beta platelet-derived growth factor (PDGF) receptor activation by PDGF-AB". J. Biol. Chem. 266 (30): 20232â7. PMID 1657917. http://www.jbc.org/cgi/content/abstract/266/30/20232.
^ Heidaran MA, Pierce JH, Jensen RA, Matsui T, Aaronson SA (5 November 1990). "Chimeric alpha- and beta-platelet-derived growth factor (PDGF) receptors define three immunoglobulin-like domains of the alpha-PDGF receptor that determine PDGF-AA binding specificity". J. Biol. Chem. 265 (31): 18741â4. PMID 2172231. http://www.jbc.org/cgi/content/abstract/265/31/18741.
^ Yu JC, Li W, Wang LM, Uren A, Pierce JH, Heidaran MA (1995). "Differential requirement of a motif within the carboxyl-terminal domain of alpha-platelet-derived growth factor (alpha PDGF) receptor for PDGF focus forming activity chemotaxis, or growth". J. Biol. Chem. 270 (13): 7033â6. doi:10.1074/jbc.270.13.7033. PMID 7706238. http://www.jbc.org/cgi/content/full/270/13/7033.
^ Hoch RV, Soriano P (2003). "Roles of PDGF in animal development". Development 130 (20): 4769â4784. doi:10.1242/dev.00721. PMID 12952899.
^ Joukov V, Pajusola K, Kaipainen A, Saksela O, Alitalo K, Olofsson B, von Euler G, Orpana A, Pettersson RF, Eriksson U (1996). "Vascular endothelial growth factor B, a novel growth factor for endothelial cells". Proc. Natl. Acad. Sci. U.S.A. 93 (6): 2567â2581. doi:10.1073/pnas.93.6.2576. PMC 39839. PMID 8637916. //www.ncbi.nlm.nih.gov/pmc/articles/PMC39839/.
^ Joukov V, Pajusola K, Kaipainen A, Chilov D, Lahtinen I, Kukk E, Saksela O, Kalkkinen N, Alitalo K (1996). "A novel vascular endothelial growth factor, VEGF-C, is a ligand for the Flt4 (VEGFR-3) and KDR (VEGFR-2) receptor tyrosine kinases". EMBO J. 15 (2): 290â298. PMC 449944. PMID 8617204. //www.ncbi.nlm.nih.gov/pmc/articles/PMC449944/.
^ Lei KJ, Alitalo K, Maglione D, Guerriero V, Viglietto G, Ferraro MG, Aprelikova O, Chou JY, Persico MG, Del Vecchio S (1993). "Two alternative mRNAs coding for the angiogenic factor, placenta growth factor (PlGF), are transcribed from a single gene of chromosome 14". Oncogene 8 (4): 925â931. PMID 7681160.
^ "PDGF Pathways". http://www.multi-targetedtherapy.com/pdgfSignaling.asp. Retrieved 2007-11-17.
^ Barres BA, Hart IK, Coles HSR, Burne JF, Voyvodic JT, Richardson WD, Raff MC (1992). "Cell Death and Control of Cell Survival in the Oligodendrocyte Lineage". Cell 70 (1): 31â46. doi:10.1016/0092-8674(92)90531-G. PMID 1623522.
^ ^a ^b Proto-Oncogene Proteins c-sis at the US National Library of Medicine Medical Subject Headings (MeSH)
^ Paul D, Lipton A, Klinger I (1971). "Serum factor requirements of normal and simian virus 40-transformed 3T3 mouse fibroplasts". Proc Natl Acad Sci U S A. 68 (3): 645â52. doi:10.1073/pnas.68.3.645. PMC 389008. PMID 5276775. //www.ncbi.nlm.nih.gov/pmc/articles/PMC389008/.
^ Shulman T, Sauer FG, Jackman RM, Chang CN, Landolfi NF (July 1997). "An antibody reactive with domain 4 of the platelet-derived growth factor beta receptor allows BB binding while inhibiting proliferation by impairing receptor dimerization". J. Biol. Chem. 272 (28): 17400â4. doi:10.1074/jbc.272.28.17400. PMID 9211881.
^ McClintock J, Chan I, Thaker S, Katial A, Taub F, Aotaki-Keen A, Hjelmeland L (1992). "Detection of c-sis proto-oncogene transcripts by direct enzyme-labeled cDNA probes and in situ hybridization". In Vitro Cell Dev Biol 28A (2): 102â8. doi:10.1007/BF02631013. PMID 1537750.
^ http://www.eurekalert.org/pub_releases/2011-10/jdrf-rmo101211.php
^ http://med.stanford.edu/ism/2011/october/kim.html

[edit] External links

platelet-derived growth factor at the US National Library of Medicine Medical Subject Headings (MeSH)
platelet-derived+growth+factor at eMedicine Dictionary

v t e Growth factors

Fibroblast	FGF receptor ligands: FGF1/FGF2/FGF5 Â· FGF3/FGF4/FGF6 Â· KGF (FGF7/FGF10/FGF22) Â· FGF8/FGF17/FGF18 Â· FGF9/FGF16/FGF20 FGF homologous factors: FGF11 Â· FGF12 Â· FGF13 Â· FGF14 hormone-like: FGF19 Â· FGF21 Â· FGF23

EGF-like domain	TGF-Î± Â· EGF Â· HB-EGF

TGFÎ² pathway	TGF-Î² (TGF-Î²1, TGF-Î²2, TGF-Î²3)

Insulin-like	IGF-1 Â· IGF-2

Platelet-derived	PDGFA Â· PDGFB Â· PDGFC Â· PDGFD

Vascular endothelial	VEGF-A Â· VEGF-B Â· VEGF-C Â· VEGF-D Â· PGF

Other	Nerve Â· Hepatocyte

B trdu: iter (nrpl/grfl/cytl/horl), csrc (lgic, enzr, gprc, igsr, intg, nrpr/grfr/cytr), itra (adap, gbpr, mapk), calc, lipd; path (hedp, wntp, tgfp+mapp, notp, jakp, fsap, hipp, tlrp)

Neoplasm: Tumor suppressor genes/proteins and Oncogenes/Proto-oncogenes

Ligand

Growth factors	ONCO: c-Sis/PDGF HGF

Receptor

Wnt signaling pathway	TSP: CDH1

Hedgehog signaling pathway	TSP: PTCH1

TGF beta signaling pathway	TSP: TGF beta receptor 2

Receptor tyrosine kinase	ONCO: ErbB/c-ErbB HER2/neu Her 3 c-Met c-Ret

JAK-STAT signaling pathway	ONCO: c-Kit Flt3

Intracellular signaling P+Ps

Wnt signaling pathway	ONCO: Beta-catenin TSP: APC

TGF beta signaling pathway	TSP: SMAD2 SMAD4

Akt/PKB signaling pathway	TSP: PTEN ONCO: c-Akt

Hippo signaling pathway	TSP: Neurofibromin 2/Merlin

MAPK/ERK pathway	TSP: Neurofibromin 1 ONCO: c-Ras HRAS c-Raf

Other/unknown	TSP: Maspin ONCO: c-Src

Nucleus

Cell cycle	TSP: p53 pRb WT1 p16/p14arf ONCO: CDK4 Cyclin D Cyclin E

DNA repair/Fanconi	TSP: BRCA1 BRCA2

Ubiquitin ligase	TSP: VHL ONCO: CBL MDM2

Transcription factor	TSP: KLF6 ONCO: AP-1 c-Fos c-Jun c-Myc

Mitochondria

Other/ungrouped

c-Bcl-2 - Notch - Stathmin

M: NEO

tsoc, mrkr

tumr, epon, para

drug (L1i/1e/V03)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

PDGF/VEGF domain Provide feedback

No Pfam abstract.

External database links

HOMSTRAD:	PDGF
PANDIT:	PF00341
PROSITE:	PDOC00222
Pseudofam:	PF00341
SCOP:	1pdg
SYSTERS:	PDGF

This tab holds annotation information from the InterPro database.

InterPro entry IPR000072

Platelet-derived growth factor (PDGF) [PUBMED:2546599, PUBMED:1425569] is a potent mitogen for cells of mesenchymal origin, including smooth muscle cells and glial cells. In both mouse and human, the PDGF signalling network consists of four ligands, PDGFA-D, and two receptors, PDGFRalpha and PDGFRbeta. All PDGFs function as secreted, disulphide-linked homodimers, but only PDGFA and B can form functional heterodimers. PDGFRs also function as homo- and heterodimers. All known PDGFs have characteristic `PDGF domains', which include eight conserved cysteines that are involved in inter- and intramolecular bonds. Alternate splicing of the A chain transcript can give rise to two different forms that differ only in their C-terminal extremity. The transforming protein of Woolly monkey sarcoma virus (WMSV) (Simian sarcoma virus), encoded by the v-sis oncogene, is derived from the B chain of PDGF.

PDGFs are mitogenic during early developmental stages, driving the proliferation of undifferentiated mesenchyme and some progenitor populations. During later maturation stages, PDGF signalling has been implicated in tissue remodelling and cellular differentiation, and in inductive events involved in patterning and morphogenesis. In addition to driving mesenchymal proliferation, PDGFs have been shown to direct the migration, differentiation and function of a variety of specialised mesenchymal and migratory cell types, both during development and in the adult animal [PUBMED:12952899]. Other growth factors in this family include vascular endothelial growth factors B and C (VEGF-B, VEGF-C) [PUBMED:8637916, PUBMED:8617204] which are active in angiogenesis and endothelial cell growth, and placenta growth factor (PlGF) which is also active in angiogenesis [PUBMED:7681160].

PDGF is structurally related to a number of other growth factors which also form disulphide-linked homo- or heterodimers.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	membrane (GO:0016020)
Molecular function	growth factor activity (GO:0008083)

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Cystine-knot (CL0079), which contains the following 9 members:

Coagulin Cys_knot DAN Hormone_6 NGF Noggin PDGF Sclerostin TGF_beta

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

Selex
Stockholm
FASTA
MSF

You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (57)	Full (855)	Representative proteomes				NCBI (797)	Meta (0)
	Seed (57)	Full (855)	RP15 (40)	RP35 (65)	RP55 (165)	RP75 (329)	NCBI (797)	Meta (0)
Jalview	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (57)	Full (855)	Representative proteomes				NCBI (797)	Meta (0)
	Seed (57)	Full (855)	RP15 (40)	RP35 (65)	RP55 (165)	RP75 (329)	NCBI (797)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (57)	Full (855)	Representative proteomes				NCBI (797)	Meta (0)
	Seed (57)	Full (855)	RP15 (40)	RP35 (65)	RP55 (165)	RP75 (329)	NCBI (797)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation

Seed source:

Prosite

Previous IDs:

none

Type:

Domain

Author:

Finn RD, Bateman A

Number in seed:

57

Number in full:

855

Average length of the domain:

80.20 aa

Average identity of full alignment:

36 %

Average coverage of the sequence by the domain:

33.29 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.8	20.8
Trusted cut-off	22.8	21.5
Noise cut-off	19.4	19.4

Model length:

82

Family (HMM) version:

12

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
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PDGF

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PDGF domain has been found. There are 99 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: PDGF (PF00341)

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Summary: PDGF/VEGF domain

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Platelet-derived growth factor Edit Wikipedia article

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PDGF/VEGF domain Provide feedback

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InterPro entry IPR000072

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