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27  structures 167  species 7  interactions 2637  sequences 95  architectures

Family: Sema (PF01403)

Summary: Sema domain

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This is the Wikipedia entry entitled "Sema domain". More...

Sema domain Edit Wikipedia article

PBB Protein SEMA3A image.jpg
Sema domain, immunoglobulin domain (Ig), short basic domain
Identifiers
Symbol Sema
Pfam PF01403
InterPro IPR001627
PROSITE PDOC51004
SCOP 1olz
SUPERFAMILY 1olz

The Sema domain is a structural domain of semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in the hepatocyte growth factor receptor (Uniprot: P08581), Plexin-A3 [1] (Uniprot: P51805) and in viral proteins.

CD100 (also called SEMA4D) is associated with PTPase and serine kinase activity. CD100 increases PMA, CD3 and CD2 induced T cell proliferation, increases CD45 induced T cell adhesion, induces B cell homotypic adhesion and down-regulates B cell expression of CD23.

The Sema domain is characterised by a conserved set of cysteine residues, which form four disulfide bonds to stabilise the structure. The Sema domain fold is a variation of the beta propeller topology, with seven blades radially arranged around a central axis. Each blade contains a four- stranded (strands A to D) antiparallel beta sheet. The inner strand of each blade (A) lines the channel at the centre of the propeller, with strands B and C of the same repeat radiating outward, and strand D of the next repeat forming the outer edge of the blade. The large size of the Sema domain is not due to a single inserted domain but results from the presence of additional secondary structure elements inserted in most of the blades. The Sema domain uses a 'loop and hook' system to close the circle between the first and the last blades. The blades are constructed sequentially with an N-terminal beta- strand closing the circle by providing the outermost strand (D) of the seventh (C-terminal) blade. The beta-propeller is further stabilized by an extension of the N-terminus, providing an additional, fifth beta-strand on the outer edge of blade 6.[2][3][4]

CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://mpr.nci.nih.gov/prow/).

Human proteins containing this domain

MET; MST1R; PLXNA1; PLXNA2; PLXNA3; PLXNA4; PLXNB1; PLXNB2; PLXNB3; PLXND1; SEMA3A; SEMA3B; SEMA3C; SEMA3D; SEMA3E; SEMA3F; SEMA3G; SEMA4A; SEMA4B; SEMA4C; SEMA4D; SEMA4F; SEMA4G; SEMA5A; SEMA5B; SEMA6A; SEMA6B; SEMA6C; SEMA6D; SEMA7A;

References

  1. ^ Goodman CS, Winberg ML, Noordermeer JN, Tamagnone L, Comoglio PM, Spriggs MK, Tessier-Lavigne M (1998). "Plexin A is a neuronal semaphorin receptor that controls axon guidance". Cell 95 (7): 903–916. doi:10.1016/S0092-8674(00)81715-8. PMID 9875845. 
  2. ^ Nikolov DB, Himanen JP, Rajashankar KR, Lu M, Antipenko A, Lesniak J, Barton WA, Hoemme C, Puschel AW, van Leyen K, Nardi-Dei V (2003). "Structure of the semaphorin-3A receptor binding module". Neuron 39 (4): 589–598. doi:10.1016/S0896-6273(03)00502-6. PMID 12925274. 
  3. ^ Stuart DI, Jones EY, Harlos K, Esnouf RM, Davis SJ, Love CA, Mavaddat N (2003). "The ligand-binding face of the semaphorins revealed by the high-resolution crystal structure of SEMA4D". Nat. Struct. Biol. 10 (10): 843–848. doi:10.1038/nsb977. PMID 12958590. 
  4. ^ Lazarus RA, Kirchhofer D, Stamos J, Yao X, Wiesmann C (2004). "Crystal structure of the HGF beta-chain in complex with the Sema domain of the Met receptor". EMBO J. 23 (12): 2325–2335. doi:10.1038/sj.emboj.7600243. PMC 423285. PMID 15167892. 

This article incorporates text from the public domain Pfam and InterPro IPR001627

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.

Sema domain Provide feedback

The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in P08581 the hepatocyte growth factor receptor and P51805

Literature references

  1. Winberg ML, Noordermeer JN, Tamagnone L, Comoglio PM, Spriggs MK, Tessier-Lavigne M, Goodman CS; , Cell 1998;95:903-916.: Plexin A is a neuronal semaphorin receptor that controls axon guidance. PUBMED:9875845 EPMC:9875845


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001627

The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in a hepatocyte growth factor receptor, in SEX protein [PUBMED:9875845] and in viral proteins.

CD100 (also called SEMA4D) is associated with PTPase and serine kinase activity. CD100 increases PMA, CD3 and CD2 induced T cell proliferation, increases CD45 induced T cell adhesion, induces B cell homotypic adhesion and down-regulates B cell expression of CD23.

The Sema domain is characterised by a conserved set of cysteine residues, which form four disulphide bonds to stabilise the structure. The Sema domain fold is a variation of the beta propeller topology, with seven blades radially arranged around a central axis. Each blade contains a four- stranded (strands A to D) antiparallel beta sheet. The inner strand of each blade (A) lines the channel at the centre of the propeller, with strands B and C of the same repeat radiating outward, and strand D of the next repeat forming the outer edge of the blade. The large size of the Sema domain is not due to a single inserted domain but results from the presence of additional secondary structure elements inserted in most of the blades. The Sema domain uses a 'loop and hook' system to close the circle between the first and the last blades. The blades are constructed sequentially with an N-terminal beta- strand closing the circle by providing the outermost strand (D) of the seventh (C-terminal) blade. The beta-propeller is further stabilised by an extension of the N terminus, providing an additional, fifth beta-strand on the outer edge of blade 6 [PUBMED:12925274, PUBMED:12958590, PUBMED:15167892].

Gene Ontology

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

Domain organisation

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

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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...

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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
(26)
Full
(2637)
Representative proteomes NCBI
(2166)
Meta
(0)
RP15
(199)
RP35
(302)
RP55
(687)
RP75
(1239)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(26)
Full
(2637)
Representative proteomes NCBI
(2166)
Meta
(0)
RP15
(199)
RP35
(302)
RP55
(687)
RP75
(1239)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(26)
Full
(2637)
Representative proteomes NCBI
(2166)
Meta
(0)
RP15
(199)
RP35
(302)
RP55
(687)
RP75
(1239)
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 View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 26
Number in full: 2637
Average length of the domain: 367.60 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 40.30 %

HMM information View help on HMM parameters

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 19.1 19.1
Trusted cut-off 19.1 19.2
Noise cut-off 19.0 19.0
Model length: 433
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 7 interactions for this family. More...

ig Trypsin Sema LRR_1 PSI LRR_adjacent TIG

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 Sema domain has been found. There are 27 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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