Letunic et al. (2017) Nucleic Acids Res doi: 10.1093/nar/gkx922
Letunic et al. (2020) Nucleic Acids Res doi: 10.1093/nar/gkaa937

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Sema semaphorin domain

SMART accession number:	SM00630
Description:	-
Interpro abstract (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) ].
GO function:	protein binding (GO:0005515)
Family alignment:	View or CHROMA formatHMM/Web logoCLUSTALW formatMSF formatFASTA formatPIR format

There are 14464 Sema domains in 14456 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Taxonomic distribution of proteins containing Sema domain.

  This tree includes only several representative species. The complete taxonomic breakdown of all proteins with Sema domain is also avaliable.

  Click on the protein counts, or double click on taxonomic names to display all proteins containing Sema domain in the selected taxonomic class.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• % proteins involved KEGG pathway ID Description 72.49 map04360 Axon guidance 3.93 map04520 Adherens junction 3.93 map05120 Epithelial cell signaling in Helicobacter pylori infection 3.93 map05210 Colorectal cancer 3.93 map04060 Cytokine-cytokine receptor interaction 3.93 map04510 Focal adhesion 3.93 map05211 Renal cell carcinoma 3.93 map05218 Melanoma This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with Sema domain which could be assigned to a KEGG orthologous group, and not all proteins containing Sema domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of Sema domains in PDB

  PDB code	Main view	Title
  1olz		The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D
  1q47		Structure of the Semaphorin 3A Receptor-Binding Module
  1shy		The Crystal Structure of HGF beta-chain in Complex with the Sema Domain of the Met Receptor.
  2uzx		Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein InlB: Crystal form I
  2uzy		Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein inlb: low resolution, Crystal form II
  3afc		Mouse Semaphorin 6A extracellular domain
  3al8		Plexin A2 / Semaphorin 6A complex
  3al9		Mouse Plexin A2 extracellular domain
  3nvn		Molecular mechanism of guidance cue recognition
  3nvq		Molecular mechanism of guidance cue recognition
  3nvx		Molecular mechanism of guidance cue recognition
  3okt		Mouse Plexin A2, extracellular domains 1-4
  3okw		Mouse Semaphorin 6A, extracellular domains 1-2
  3oky		Plexin A2 in complex with Semaphorin 6A
  3ol2		Receptor-ligand structure of Human Semaphorin 4D with Plexin B1.
  4fww		Crystal structure of the Sema-PSI extracellular domains of human RON receptor tyrosine kinase
  4gz8		Mouse Semaphorin 3A, domains Sema-PSI-IG
  4gza		Complex of mouse Plexin A2 - Semaphorin 3A - Neuropilin-1
  4k3j		Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta
  4o3t		4O3T
  4o3u		4O3U
  4qt8		4QT8
  5l56		5L56
  5l59		5L59
  5l5c		5L5C
  5l5g		5L5G
  5l5k		5L5K
  5l5l		5L5L
  5l5m		5L5M
  5l5n		5L5N

• Links (links to other resources describing this domain)

• INTERPRO	IPR001627

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