Summary: Ephrin

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Ephrin Edit Wikipedia article

Ephrin

structural and biophysical characterization of the ephb4-ephrinb2 protein protein interaction and receptor specificity.

Identifiers

Symbol

Ephrin

Pfam clan

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

Ephrins also known as ephrin ligands or Eph family receptor interacting proteins are a family of proteins that serve as the ligands of the ephrin receptor. Ephrin receptors in turn compose the largest known subfamily of receptor protein-tyrosine kinases (RTKs).

Since ephrin ligands (ephrins) and Eph receptors (Ephs) are both membrane-bound proteins, binding and activation of Eph/epherin intracellular signaling pathways can only occur via direct cell-cell interaction. Eph/epherin signaling regulates a variety of biological processes during embryonic development including the guidance of axon growth cones,^[1] formation of tissue boundaries,^[2] cell migration, and segmentation.^[3] Additionally, Eph/epherin signaling has recently been identified to play a critical role in the maintenance of several processes during adulthood including long-term potentiation,^[4] angiogenesis,^[5] and stem cell differentiation.^[6]

[edit] Classification

Ephrin ligands are divided into two subclasses of ephrin-A and ephrin-B based on their structure and linkage to the cell membrane. Ephrin-As are anchored to the membrane by a glycosylphosphatidylinositol (GPI) linkage and lack a cytoplasmic domain while ephrin-Bs are attached to the membrane by a single transmembrane domain that contains a short cytoplasmic PDZ-binding motif. The genes that encode the ephrin-A and ephrin-B proteins are designated as EFNA and EFNB respectively. Eph receptors in turn are classified as either EphAs or EphBs based on their binding affinity for either the ephrin-A or ephrin-B ligands.^[7]

Of the eight ephrins that have been identified in humans there are five known ephrin-A ligands (ephrin-A1-5) that interact with nine EphAs (EphA1-8 and EphA10) and three ephrin-B ligands (ephrin-B1-3) that interact with five EphBs (EphB1-4 and EphB6).^[4]^[8] Ephs of a particular subclass demonstrate an ability to bind with high affinity to all ephrins of the corresponding subcass, but in general have little to no cross-binding to ephrins of the opposing subclass.^[9] However, there are a few exceptions to this intrasubclass binding specificity as it has recently been shown that ephrin-B3 is able bind to and activate EPH receptor A4 and ephrin-A5 can bind to and activate Eph receptor B2.^[10] EphAs/ephrin-As typically bind with high affinity, which can partially be attributed to the fact that ephrinAs interact with EphAs by a "lock-and-key" mechanism that requires little conformational change of the EphAs upon ligand binding. In contrast EphBs typically bind with lower affinity than EphAs/ephring-As since they utilize an "induced fit" mechanism that requires a greater conformational change of EphBs to bind ephrin-Bs.^[11]

[edit] Function

[edit] Axon guidance

During the development of the central nervous system Eph/ephrin signaling plays a critical role in the cell-cell mediated migration of several types of neuronal axons to their target destinations. Eph/ephrin signaling controls the guidance of neuronal axons through their ability to inhibit the survival of axonal growth cones, which repels the migrating axon away from the site of Eph/ephrin activation.^[12] The growth cones of migrating axons do not simply respond to absolute levels of Ephs or ephrins in cells that they contact, but rather respond to relative levels of Eph and ephrin expression,^[13] which allows migrating axons that express either Ephs or ephrins to be directed along gradients of Eph or ephrin expressing cells towards a destination where axonal growth cone survival is no longer completely inhibited.^[12]

Although Eph-ephrin activation is usually associated with decreased growth cone survival and the repellence of migrating axons, it has recently been demonstrated that growth cone survival does not depend just on Eph-ephrin activation, but rather on the differential effects of "forward" signaling by the Eph receptor or "reverse" signaling by the ephrin ligand on growth cone survival^[12]^[14](see "Ephrin Reverse Signaling" below).

[edit] Retinotopic mapping

The formation of an organized retinotopic map in the superior colliculus (SC) (referred to as the optic tectum in lower vertebrates) requires the proper migration of the axons of retinal ganglion cells (RGCs) from the retina to specific regions in the SC that is mediated by gradients of Eph and ephrin expression in both the SC and in migrating RGCs leaving the retina.^[15] The decreased survival of axonal growth cones discussed above allows for a gradient of high posterior to low anterior ephrin-A ligand expression in the SC to direct migrating RGCs axons from the temporal region of the retina that express a high level of EphA receptors toward targets in the anterior SC and RGCs from the nasal retina that have low EphA expression toward their final destination in the posterior SC.^[16]^[17]^[18] Similarly, a gradient of ephrin-B1 expression along the medial-ventral axis of the SC directs the migration of dorsal and ventral EphB-expressing RGCs to the lateral and medial SC respectively.^[19]

[edit] Reverse signaling

One unique property of the ephrin ligands is that many have the capacity to initiate a "reverse" signal that is separate and distinct from the intracellular signal activated in Eph receptor-expressing cells. Although the mechanisms by which "reverse" signaling occurs are not completely understood, both ephrin-As and ephrin-Bs have been shown to mediate cellular responses that are distinct from those associated with activation of their corresponding receptors. Specifically, ephrin-A5 was shown to stimulate growth cone spreading in spinal motor neurons^[12] and ephrin-B1 was shown to promote dendritic spine maturation.^[20]

[edit] References

^ Egea, J.; Klein, R. D. (2007). "Bidirectional Eph–ephrin signaling during axon guidance". Trends in Cell Biology 17 (5): 230–238. doi:10.1016/j.tcb.2007.03.004. PMID 17420126. edit
^ Rohani, N.; Canty, L.; Luu, O.; Fagotto, F. O.; Winklbauer, R. (2011). "EphrinB/EphB Signaling Controls Embryonic Germ Layer Separation by Contact-Induced Cell Detachment". In Hamada, Hiroshi. PLoS Biology 9 (3): e1000597. doi:10.1371/journal.pbio.1000597. PMC 3046958. PMID 21390298. edit
^ Davy, A.; Soriano, P. (2005). "Ephrin signaling in vivo: Look both ways". Developmental Dynamics 232 (1): 1–10. doi:10.1002/dvdy.20200. PMID 15580616. edit
^ ^a ^b Kullander, K.; Klein, R. D. (2002). "Mechanisms and functions of eph and ephrin signalling". Nature Reviews Molecular Cell Biology 3 (7): 475–486. doi:10.1038/nrm856. PMID 12094214. edit
^ Kuijper, S.; Turner, C. J.; Adams, R. H. (2007). "Regulation of Angiogenesis by Eph–Ephrin Interactions". Trends in Cardiovascular Medicine 17 (5): 145–151. doi:10.1016/j.tcm.2007.03.003. PMID 17574121. edit
^ Genander, M.; Frisén, J. (2010). "Ephrins and Eph receptors in stem cells and cancer". Current Opinion in Cell Biology 22 (5): 611–616. doi:10.1016/j.ceb.2010.08.005. PMID 20810264. edit
^ Ephnomenclaturecommittee (1997). "Unified nomenclature for Eph family receptors and their ligands, the ephrins. Eph Nomenclature Committee". Cell 90 (3): 403–404. doi:10.1016/S0092-8674(00)80500-0. PMID 9267020. edit
^ Pitulescu, M. E.; Adams, R. H. (2010). "Eph/ephrin molecules—a hub for signaling and endocytosis". Genes & Development 24 (22): 2480–2492. doi:10.1101/gad.1973910. PMC 2975924. PMID 21078817. edit
^ Pasquale, E. B. (1997). "The Eph family of receptors". Current opinion in cell biology 9 (5): 608–615. doi:10.1016/S0955-0674(97)80113-5. PMID 9330863. edit
^ Himanen, J. P.; Chumley, M. J.; Lackmann, M.; Li, C.; Barton, W. A.; Jeffrey, P. D.; Vearing, C.; Geleick, D. et al. (2004). "Repelling class discrimination: Ephrin-A5 binds to and activates EphB2 receptor signaling". Nature Neuroscience 7 (5): 501–509. doi:10.1038/nn1237. PMID 15107857. |displayauthors= suggested (help) edit
^ Himanen, J. P. (2011). "Ectodomain structures of Eph receptors". Seminars in Cell & Developmental Biology 23 (1): 35–42. doi:10.1016/j.semcdb.2011.10.025. PMID 22044883. edit
^ ^a ^b ^c ^d Marquardt, T.; Shirasaki, R.; Ghosh, S.; Andrews, S. E.; Carter, N.; Hunter, T.; Pfaff, S. L. (2005). "Coexpressed EphA Receptors and Ephrin-A Ligands Mediate Opposing Actions on Growth Cone Navigation from Distinct Membrane Domains". Cell 121 (1): 127–139. doi:10.1016/j.cell.2005.01.020. PMID 15820684. edit
^ Reber, M. L.; Burrola, P.; Lemke, G. (2004). "A relative signalling model for the formation of a topographic neural map". Nature 431 (7010): 847–853. doi:10.1038/nature02957. PMID 15483613. edit
^ Petros, T. J.; Bryson, J. B.; Mason, C. (2010). "Ephrin-B2 elicits differential growth cone collapse and axon retraction in retinal ganglion cells from distinct retinal regions". Developmental Neurobiology 70 (11): 781–794. doi:10.1002/dneu.20821. PMC 2930402. PMID 20629048. edit
^ Triplett, J. W.; Feldheim, D. A. (2011). "Eph and ephrin signaling in the formation of topographic maps". Seminars in Cell & Developmental Biology 23 (1): 7–15. doi:10.1016/j.semcdb.2011.10.026. PMID 22044886. edit
^ Wilkinson, D. G. (2001). "Multiple roles of EPH receptors and ephrins in neural development". Nature Reviews Neuroscience 2 (3): 155–164. doi:10.1038/35058515. PMID 11256076. edit
^ Cheng, H. J.; Nakamoto, M.; Bergemann, A. D.; Flanagan, J. G. (1995). "Complementary gradients in expression and binding of ELF-1 and Mek4 in development of the topographic retinotectal projection map". Cell 82 (3): 371–381. doi:10.1016/0092-8674(95)90426-3. PMID 7634327. edit
^ Drescher, U.; Kremoser, C.; Handwerker, C.; Löschinger, J.; Noda, M.; Bonhoeffer, F. (1995). "In vitro guidance of retinal ganglion cell axons by RAGS, a 25 kDa tectal protein related to ligands for Eph receptor tyrosine kinases". Cell 82 (3): 359–370. doi:10.1016/0092-8674(95)90425-5. PMID 7634326. edit
^ Mann, F.; Ray, S.; Harris, W.; Holt, C. (2002). "Topographic mapping in dorsoventral axis of the Xenopus retinotectal system depends on signaling through ephrin-B ligands". Neuron 35 (3): 461–473. doi:10.1016/S0896-6273(02)00786-9. PMID 12165469. edit
^ Segura, I.; Essmann, C. L.; Weinges, S.; Acker-Palmer, A. (2007). "Grb4 and GIT1 transduce ephrinB reverse signals modulating spine morphogenesis and synapse formation". Nature Neuroscience 10 (3): 301–310. doi:10.1038/nn1858. PMID 17310244. edit

v t e Intercellular signaling peptides and proteins / ligands

Growth factors	Endothelial growth factor Epidermal growth factor Fibroblast growth factor Nerve growth factor Platelet-derived growth factor Transforming growth factor beta superfamily

Ephrin	EFNA1 EFNA2 EFNA3 EFNA4 EFNA5 EFNB1 EFNB2 EFNB3

Other	Adipokine Agouti signaling protein Agouti-related protein Angiogenic protein CCN intercellular signaling protein Cysteine-rich protein 61 Connective tissue growth factor Nephroblastoma overexpressed protein Cytokine Endothelin EDN1 EDN2 EDN3 Hedgehog protein Interferon Kinin Parathyroid hormone-related protein Semaphorin Somatomedin Tolloid-like metalloproteinase Tumor necrosis factor Wnt protein

see also extracellular ligand disorders 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)

This article incorporates text from the public domain Pfam and InterPro IPR001799

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.

Ephrin Provide feedback

No Pfam abstract.

External database links

PANDIT:	PF00812
PROSITE:	PDOC01003
Pseudofam:	PF00812
SCOP:	1kgy
SYSTERS:	Ephrin

This tab holds annotation information from the InterPro database.

InterPro entry IPR001799

Ephrins are a family of proteins [PUBMED:7838529] that are ligands of class V (EPH-related) receptor protein-tyrosine kinases. These receptors and their ligands have been implicated in regulating neuronal axon guidance and in patterning of the developing nervous system and may also serve a patterning and compartmentalisation role outside of the nervous system as well.

Ephrins are membrane-attached proteins of 205 to 340 residues. Attachment appears to be crucial for their normal function. Type-A ephrins are linked to the membrane via a glycosylphosphatidylinositol (GPI)-linkage, while type-B ephrins are type-I membrane proteins.

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)

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 CU_oxidase (CL0026), which contains the following 9 members:

Copper-bind COX2 Cu-oxidase Cu-oxidase_2 Cu-oxidase_3 Cu_bind_like Cupredoxin_1 Ephrin SoxE

Alignments

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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

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Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

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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 (14)	Full (554)	Representative proteomes				NCBI (430)	Meta (1)
	Seed (14)	Full (554)	RP15 (47)	RP35 (74)	RP55 (164)	RP75 (288)	NCBI (430)	Meta (1)
Jalview	View	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 (14)	Full (554)	Representative proteomes				NCBI (430)	Meta (1)
	Seed (14)	Full (554)	RP15 (47)	RP35 (74)	RP55 (164)	RP75 (288)	NCBI (430)	Meta (1)
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 (14)	Full (554)	Representative proteomes				NCBI (430)	Meta (1)
	Seed (14)	Full (554)	RP15 (47)	RP35 (74)	RP55 (164)	RP75 (288)	NCBI (430)	Meta (1)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	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:

Pfam-B_1390 (release 2.1)

Previous IDs:

none

Type:

Family

Author:

Bateman A

Number in seed:

14

Number in full:

554

Average length of the domain:

131.80 aa

Average identity of full alignment:

39 %

Average coverage of the sequence by the domain:

52.16 %

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	25.0	25.0
Trusted cut-off	25.2	25.7
Noise cut-off	24.8	23.8

Model length:

146

Family (HMM) version:

12

Download:

download the raw HMM for this family

Species distribution

Sunburst
Tree

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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.

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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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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.

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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.

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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 Ephrin domain has been found. There are 31 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: Ephrin (PF00812)

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