Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
94  structures 493  species 0  interactions 18177  sequences 308  architectures

Family: Sema (PF01403)

Summary: Sema domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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
SymbolSema
PfamPF01403
InterProIPR001627
PROSITEPDOC51004
SCOP21olz / SCOPe / SUPFAM
Membranome71

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]

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. ^ Winberg ML, Noordermeer JN, Tamagnone L, Comoglio PM, Spriggs MK, Tessier-Lavigne M, Goodman CS (December 1998). "Plexin A is a neuronal semaphorin receptor that controls axon guidance". Cell. 95 (7): 903–16. doi:10.1016/S0092-8674(00)81715-8. PMID 9875845. S2CID 14703056.
  2. ^ Antipenko A, Himanen JP, van Leyen K, Nardi-Dei V, Lesniak J, Barton WA, Rajashankar KR, Lu M, Hoemme C, Püschel AW, Nikolov DB (August 2003). "Structure of the semaphorin-3A receptor binding module". Neuron. 39 (4): 589–98. doi:10.1016/S0896-6273(03)00502-6. PMID 12925274. S2CID 9782923.
  3. ^ Love CA, Harlos K, Mavaddat N, Davis SJ, Stuart DI, Jones EY, Esnouf RM (October 2003). "The ligand-binding face of the semaphorins revealed by the high-resolution crystal structure of SEMA4D". Nature Structural Biology. 10 (10): 843–8. doi:10.1038/nsb977. PMID 12958590. S2CID 24468463.
  4. ^ Stamos J, Lazarus RA, Yao X, Kirchhofer D, Wiesmann C (June 2004). "Crystal structure of the HGF beta-chain in complex with the Sema domain of the Met receptor". The EMBO Journal. 23 (12): 2325–35. 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 plexins [ PUBMED:9875845 ], receptors for multiple classes of semaphorins, in hepatocyte growth factor receptor, and in viral proteins [ PUBMED:9712866 ].

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan Beta_propeller (CL0186), which has the following description:

This large clan contains proteins that contain beta propellers. These are composed of between 6 and 8 repeats. The individual repeats are composed of a four stranded sheet. The clan includes families such as WD40 Pfam:PF00400 where the individual repeats are modeled. The clan also includes families where the entire propeller is modeled such as Pfam:PF02239 usually because the individual repeats are not discernible. These proteins carry out a very wide diversity of functions including catalysis.

The clan contains the following 112 members:

ANAPC1 ANAPC4_WD40 Arylesterase Arylsulfotran_2 Arylsulfotrans B_lectin BBS2_Mid BBS2_N Beta_propel Coatomer_WDAD CPSF_A CyRPA Cytochrom_D1 DCAF17 Dpp_8_9_N DPPIV_N DPPIV_rep DUF1513 DUF1668 DUF2415 DUF346 DUF3466 DUF3616 DUF3748 DUF4221 DUF4374 DUF4394 DUF4623 DUF4784 DUF4915 DUF4933 DUF4934 DUF5046 DUF5050 DUF5122 DUF5128 DUF5711 DUF839 eIF2A FG-GAP FG-GAP_2 FG-GAP_3 Frtz Ge1_WD40 Glu_cyclase_2 Glyoxal_oxid_N Gmad1 GSDH Helveticin_J HPS3_N HPS6 Hyd_WA IKI3 Itfg2 Kelch_1 Kelch_2 Kelch_3 Kelch_4 Kelch_5 Kelch_6 Lactonase Ldl_recept_b LGFP Lgl_C LVIVD Me-amine-dh_H MgpC MRJP Nbas_N NBCH_WD40 Neisseria_PilC NHL nos_propeller nos_propeller_2 Nucleoporin_N Nup160 Nup88 P1_N PALB2_WD40 PD40 Pectate_lyase22 Peptidase_S9_N PHTB1_N Phytase-like PQQ PQQ_2 PQQ_3 RAB3GAP2_N RAG2 RCC1 RCC1_2 Reg_prop RPE65 SBBP SBP56 SdiA-regulated Sema SGL SSL_N Str_synth TcdB_toxin_midN Tectonin TolB_like VID27 Vps16_N WD40 WD40_2 WD40_3 WD40_4 WD40_like WDCP YmzC

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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
(191)
Full
(18177)
Representative proteomes UniProt
(28737)
RP15
(1491)
RP35
(4498)
RP55
(13195)
RP75
(18352)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(191)
Full
(18177)
Representative proteomes UniProt
(28737)
RP15
(1491)
RP35
(4498)
RP55
(13195)
RP75
(18352)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(191)
Full
(18177)
Representative proteomes UniProt
(28737)
RP15
(1491)
RP35
(4498)
RP55
(13195)
RP75
(18352)
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.

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: Repeat
Sequence Ontology: SO:0001068
Author: Bateman A
Number in seed: 191
Number in full: 18177
Average length of the domain: 176.10 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 16.80 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.7 23.7
Trusted cut-off 23.7 23.7
Noise cut-off 23.6 23.6
Model length: 180
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 94 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.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JZC4 View 3D Structure Click here
A0A0G2K0S6 View 3D Structure Click here
A0A0G2KLL0 View 3D Structure Click here
A0A0G2KQ30 View 3D Structure Click here
A0A0G2LB43 View 3D Structure Click here
A0A0R4IR66 View 3D Structure Click here
A0A0R4IRZ9 View 3D Structure Click here
A0A140LGG1 View 3D Structure Click here
A0A286YAK7 View 3D Structure Click here
A0A2R8Q0R5 View 3D Structure Click here
A0A2R8Q3J7 View 3D Structure Click here
A0A2R8Q5T8 View 3D Structure Click here
A0A2R8QAH3 View 3D Structure Click here
A0A2R8QFP9 View 3D Structure Click here
A0A2R8QGT5 View 3D Structure Click here
A0A2R8QPJ6 View 3D Structure Click here
A0A2R8RWP0 View 3D Structure Click here
A0A2R9YJJ7 View 3D Structure Click here
A0M8R7 View 3D Structure Click here
A0M8S8 View 3D Structure Click here
A1L5C9 View 3D Structure Click here
A3KPS4 View 3D Structure Click here
A7MB70 View 3D Structure Click here
B0S5N4 View 3D Structure Click here
B2RXS4 View 3D Structure Click here
B8JHX0 View 3D Structure Click here
B8JMB1 View 3D Structure Click here
D3Z8E2 View 3D Structure Click here
D3Z981 View 3D Structure Click here
D3ZAG0 View 3D Structure Click here
D3ZDX5 View 3D Structure Click here
D3ZES7 View 3D Structure Click here
D3ZHJ3 View 3D Structure Click here
D3ZLH5 View 3D Structure Click here
D3ZPX4 View 3D Structure Click here
D3ZQ57 View 3D Structure Click here
D3ZQP6 View 3D Structure Click here
D3ZTD8 View 3D Structure Click here
D3ZWP6 View 3D Structure Click here
D3ZYM4 View 3D Structure Click here