Summary: Ephrin receptor ligand binding domain
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This is the Wikipedia entry entitled "Ephrin receptor". More...
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Ephrin receptor ligand binding domain Provide feedback
The Eph receptors, which bind to ephrins PF00812 are a large family of receptor tyrosine kinases. This family represents the amino terminal domain which binds the ephrin ligand [1].
Literature references
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Himanen JP, Henkemeyer M, Nikolov DB; , Nature 1998;396:486-491.: Crystal structure of the ligand-binding domain of the receptor tyrosine kinase EphB2. PUBMED:9853759 EPMC:9853759
External database links
SCOP: | 1nuk |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001090
The Eph receptors, which bind a group of cell-membrane-anchored ligands known as ephrins, represent the largest subfamily of receptor tyrosine kinases (RTKs). The Eph receptors and their ephrin ligands control a diverse array of cell-cell interactions in the nervous and vascular systems. On ephrin binding, the Eph kinase domain is activated, initiating 'forward' signaling in the receptor-expressing cells. Simultaneously, signals are also induced in the ligand-expressing cells a phenomenon referred to as 'reverse' signalling. The extracellular Eph receptor region contains a conserved 180- amino-acid N-terminal ligand-binding domain (LBD) which is both necessary and sufficient for bindings of the receptors to their ephrin ligands. An adjacent cysteine-rich region might be involved in receptor-receptor oligomerization often observed on ligand binding, whereas the next two fibronectin type III repeats have yet to be assigned a clear biological function. The cytoplasmic Eph receptor region contains a kinase domain, a sterile alpha motif (SAM) domain, and a PDZ-binding motif. The ligand-binding domain (LBD) of Eph receptors is unique to this family of RTKs ans shares no significant amino-acid-sequence homology with other known proteins [PUBMED:9853759, PUBMED:11780069, PUBMED:19525919].
The Eph LBD domain forms a compact globular structure which folds into a jellyroll beta-sandwich composed of 11 antiparallel beta-strands. It has two antiparallel beta-sheets, with the usual left-handed twist, packed against each other to form a compact beta-sandwich, and a short 3(10) helix [PUBMED:9853759, PUBMED:11780069, PUBMED:19525919].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | protein binding (GO:0005515) |
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 GBD (CL0202), which has the following description:
This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].
The clan contains the following 70 members:
7TMR-DISMED2 Agarase_CBM Allantoicase ANAPC10 Arabino_trans_C Bac_rhamnosid_N BcsB BetaGal_dom4_5 BPA_C Calpain_III CBM-like CBM27 CBM32 CBM46 CBM60 CBM65_1 CBM_11 CBM_15 CBM_17_28 CBM_26 CBM_35 CBM_4_9 CBM_6 CE2_N CIA30 Clenterotox Cry1Ac_D5 DUF4465 DUF4627 DUF5000 DUF5010_C DUF5077 DUF5625 DUF642 Endotoxin_C Ephrin_lbd Exop_C F5_F8_type_C FBA FlhE GH101_N GH115_C Glft2_N Glyco_hydro_2_N GxDLY HA70_C Laminin_B Laminin_N Lectin_like Lipl32 Lyase_N Malectin Malectin_like Muskelin_N NPCBM P_proprotein PA-IL PAW PCMD PepX_C PINIT PITH PPC PulA_N1 Sad1_UNC SGBP_B_XBD TcA_TcB_BD Thioredoxin_10 XRCC1_N YpMAlignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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 (60) |
Full (4099) |
Representative proteomes | UniProt (6176) |
NCBI (11942) |
Meta (0) |
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RP15 (259) |
RP35 (952) |
RP55 (2748) |
RP75 (4307) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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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 (60) |
Full (4099) |
Representative proteomes | UniProt (6176) |
NCBI (11942) |
Meta (0) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (259) |
RP35 (952) |
RP55 (2748) |
RP75 (4307) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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: | [1] |
Previous IDs: | EPH_lbd; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 60 |
Number in full: | 4099 |
Average length of the domain: | 169.60 aa |
Average identity of full alignment: | 53 % |
Average coverage of the sequence by the domain: | 19.58 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 178 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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_lbd domain has been found. There are 97 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 sequence.
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