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82  structures 432  species 0  interactions 14901  sequences 323  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
SymbolSema
PfamPF01403
InterProIPR001627
PROSITEPDOC51004
SCOPe1olz / 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.
  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.
  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.
  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


Internal database links

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...

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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(202)
Full
(14901)
Representative proteomes UniProt
(24466)
RP15
(1418)
RP35
(4648)
RP55
(12609)
RP75
(16642)
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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
(202)
Full
(14901)
Representative proteomes UniProt
(24466)
RP15
(1418)
RP35
(4648)
RP55
(12609)
RP75
(16642)
Alignment:
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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
(202)
Full
(14901)
Representative proteomes UniProt
(24466)
RP15
(1418)
RP35
(4648)
RP55
(12609)
RP75
(16642)
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: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 202
Number in full: 14901
Average length of the domain: 384.90 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 39.43 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -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 23.5 23.6
Model length: 420
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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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 Sema domain has been found. There are 82 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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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
A1L5C9 View 3D Structure Click here
A3KPS4 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
D3ZYR4 View 3D Structure Click here
D4A6G2 View 3D Structure Click here
D4A9J3 View 3D Structure Click here
D4AA77 View 3D Structure Click here
D4AEM7 View 3D Structure Click here
E3W9A6 View 3D Structure Click here
E7EYX4 View 3D Structure Click here
E7F898 View 3D Structure Click here
E7FBE1 View 3D Structure Click here
E7FGY1 View 3D Structure Click here
F1LNH0 View 3D Structure Click here
F1LSV0 View 3D Structure Click here
F1MAG8 View 3D Structure Click here
F1Q5G8 View 3D Structure Click here
F1Q6L2 View 3D Structure Click here
F1Q7U0 View 3D Structure Click here
F1QBC0 View 3D Structure Click here
F1QF70 View 3D Structure Click here
F1QJZ8 View 3D Structure Click here
F1QLR7 View 3D Structure Click here
F1QPG9 View 3D Structure Click here
F1QPQ6 View 3D Structure Click here
F1QR50 View 3D Structure Click here
F1QU86 View 3D Structure Click here
F1R501 View 3D Structure Click here
F1R9L1 View 3D Structure Click here
F1RB05 View 3D Structure Click here
F7F3I7 View 3D Structure Click here
F7FHT4 View 3D Structure Click here
F8W238 View 3D Structure Click here
F8W2F8 View 3D Structure Click here
F8W2K2 View 3D Structure Click here
M9MM94 View 3D Structure Click here
M9MM97 View 3D Structure Click here
M9MMA2 View 3D Structure Click here
O08665 View 3D Structure Click here
O09126 View 3D Structure Click here
O15031 View 3D Structure Click here
O15041 View 3D Structure Click here
O35464 View 3D Structure Click here
O43157 View 3D Structure Click here
O45657 View 3D Structure Click here
O54951 View 3D Structure Click here
O70141 View 3D Structure Click here
O75051 View 3D Structure Click here
O75326 View 3D Structure Click here
O88632 View 3D Structure Click here
O95025 View 3D Structure Click here
O95754 View 3D Structure Click here
P08581 View 3D Structure Click here
P16056 View 3D Structure Click here
P51805 View 3D Structure Click here
P70206 View 3D Structure Click here
P70207 View 3D Structure Click here
P70208 View 3D Structure Click here
P70275 View 3D Structure Click here
P97523 View 3D Structure Click here
Q04912 View 3D Structure Click here
Q13214 View 3D Structure Click here
Q13275 View 3D Structure Click here
Q13591 View 3D Structure Click here
Q14563 View 3D Structure Click here
Q17330 View 3D Structure Click here
Q1LVE1 View 3D Structure Click here
Q1LYS1 View 3D Structure Click here
Q24322 View 3D Structure Click here
Q24323 View 3D Structure Click here
Q3UH93 View 3D Structure Click here
Q4LFA9 View 3D Structure Click here
Q5RH90 View 3D Structure Click here
Q5RHX7 View 3D Structure Click here
Q60519 View 3D Structure Click here
Q62177 View 3D Structure Click here
Q62178 View 3D Structure Click here
Q62179 View 3D Structure Click here
Q62181 View 3D Structure Click here
Q62190 View 3D Structure Click here
Q62217 View 3D Structure Click here
Q63548 View 3D Structure Click here
Q64151 View 3D Structure Click here
Q6BEA0 View 3D Structure Click here
Q76KF0 View 3D Structure Click here
Q7KK54 View 3D Structure Click here
Q80UG2 View 3D Structure Click here
Q8BH34 View 3D Structure Click here
Q8CJH3 View 3D Structure Click here
Q8NFY4 View 3D Structure Click here
Q92854 View 3D Structure Click here
Q95XP4 View 3D Structure Click here
Q99985 View 3D Structure Click here
Q9C0C4 View 3D Structure Click here
Q9H2E6 View 3D Structure Click here
Q9H3S1 View 3D Structure Click here
Q9H3T2 View 3D Structure Click here
Q9H3T3 View 3D Structure Click here
Q9HCM2 View 3D Structure Click here
Q9NPR2 View 3D Structure Click here
Q9NS98 View 3D Structure Click here
Q9NTN9 View 3D Structure Click here
Q9P283 View 3D Structure Click here
Q9QUR8 View 3D Structure Click here
Q9QY40 View 3D Structure Click here
Q9TYS4 View 3D Structure Click here
Q9UIW2 View 3D Structure Click here
Q9ULL4 View 3D Structure Click here
Q9V491 View 3D Structure Click here
Q9V4A7 View 3D Structure Click here
Q9VTT0 View 3D Structure Click here
Q9W686 View 3D Structure Click here
Q9W6G6 View 3D Structure Click here
Q9W7J1 View 3D Structure Click here
Q9WTL3 View 3D Structure Click here
Q9WTM3 View 3D Structure Click here
Q9WUH7 View 3D Structure Click here
Q9Y4D7 View 3D Structure Click here
Q9YHX4 View 3D Structure Click here
Q9Z123 View 3D Structure Click here
Q9Z143 View 3D Structure Click here
U4PRY7 View 3D Structure Click here