Summary: Lectin C-type domain
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C-type lectin Edit Wikipedia article
|Lectin C-type domain|
Pentameric structure of rattlesnake venom lectin which is a galactose binding lectin.
A C-type lectin (CLEC) is a type of carbohydrate-binding protein domain known as a lectin. The C-type designation is from their requirement for calcium for binding. Proteins that contain C-type lectin domains have a diverse range of functions including cell-cell adhesion, immune response to pathogens and apoptosis.
Drickamer et al. classified C-type lectins into 7 subgroups (I to VII) based on the order of the various protein domains in each protein. This classification was subsequently updated in 2002, leading to seven additional groups (VIII to XIV). Most recently, three further subgroups were added (XV to XVII).
|I||Lecticans||EGF, Sushi, Ig and Link domains|
|II||Asialoglycoprotein and DC receptors||None|
|IV||Selectins||Sushi and EGF domains|
|V||NK - cell receptors||None|
|VI||Multi-CTLD endocytic receptors||FnII and Ricin domains|
|X||Polycystin||WSC, REJ, PKD domains|
|XI||Attractin (ATRN)||PSI, EGF and CUB domains|
|XII||Eosinophil major basic protein (EMBP)||None|
|XIV||Thrombomodulin, CD93, CD248||EGF domains|
|XVI||SEEC||SCP and EGF domains|
|XVII||CBCP/Frem1/QBRICK||CSPG repeats and CalX-beta domains|
- CLEC1A, CLEC1B
- CLEC2A, CLEC2B, CD69 (CLEC2C), CLEC2D, CLEC2L
- CLEC3A, CLEC3B
- CLEC4A, CLEC4C, CLEC4D, CLEC4E, CLEC4F, CLEC4G, ASGR1 (CLEC4H1), ASGR2 (CLEC4H2), FCER2 (CLEC4J), CD207 (CLEC4K), CD209 (CLEC4L), CLEC4M
- OLR1 (CLEC8A)
- CLEC12A, CLEC12B
- CD302 (CLEC13A), LY75 (CLEC13B), PLA2R1 (CLEC13C), MRC1 (CLEC13D), MRC2 (CLEC13E)
The "NK Cell lectin-like receptors" are a very closely related group:
- KLRB1 (CLEC5B)
- KLRC1, KLRC2, KLRC3, KLRC4
- KLRF1 (CLEC5C)
- KLRG1 (CLEC15A), KLRG2 (CLEC15B)
Additional proteins containing this domain include:
- AGC1; ATRNL1
- CD248; CD72; CD93; CHODL; CL-K1-Ia; CL-K1-Ib; CL-K1-Ic; CLECSF5; COLEC10; COLEC11; COLEC12; CSPG3
- FCER2; FREM1; HBXBP;
- LAYN; LOC348174; LOC728276
- MAFA; MBL2; MGC34761; MICL; MRC1L1
- PAP; PKD1; PKD1L2; PLA2R1; PRG2; PRG3
- REG1A; REG1B; REG3A; REG3G; REG4
- SELE; SELL; SELP; SFTPA1; SFTPA2; SFTPA2B; SFTPD; SRCL
- Walker JR, Nagar B, Young NM, Hirama T, Rini JM (April 2004). "X-ray crystal structure of a galactose-specific C-type lectin possessing a novel decameric quaternary structure". Biochemistry. 43 (13): 3783–92. doi:10.1021/bi035871a. PMID 15049685.
- Zelensky AN, Gready JE (December 2005). "The C-type lectin-like domain superfamily". FEBS J. 272 (24): 6179–217. doi:10.1111/j.1742-4658.2005.05031.x. PMID 16336259.
- C-Type Lectin at the US National Library of Medicine Medical Subject Headings (MeSH)
- Drickamer K (October 1999). "C-type lectin-like domains". Curr. Opin. Struct. Biol. 9 (5): 585–90. doi:10.1016/S0959-440X(99)00009-3. PMID 10508765.
- Cambi A, Figdor C (May 2009). "Necrosis: C-type lectins sense cell death". Curr. Biol. 19 (9): R375–8. doi:10.1016/j.cub.2009.03.032. PMID 19439262.
- Drickamer K (1993). "Evolution of Ca(2+)-dependent animal lectins". Prog. Nucleic Acid Res. Mol. Biol. Progress in Nucleic Acid Research and Molecular Biology. 45: 207–32. doi:10.1016/S0079-6603(08)60870-3. ISBN 978-0-12-540045-9. PMID 8341801.
- Drickamer K, Fadden AJ (2002). "Genomic analysis of C-type lectins". Biochem. Soc. Symp. (69): 59–72. PMID 12655774.
- NK Cell Lectin-Like Receptors at the US National Library of Medicine Medical Subject Headings (MeSH)
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.
Lectin C-type domain Provide feedback
This family includes both long and short form C-type
Hakansson K, Lim NK, Hoppe HJ, Reid KB; , Structure Fold Des 1999;7:255-264.: Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D. PUBMED:10368295 EPMC:10368295
Internal database links
|SCOOP:||Xlink DUF333 UL45 Chordopox_A33R Intimin_C DUF5075|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001304
Lectins occur in plants, animals, bacteria and viruses. Initially described for their carbohydrate-binding activity [PUBMED:14533786], they are now recognised as a more diverse group of proteins, some of which are involved in protein-protein, protein-lipid or protein-nucleic acid interactions [PUBMED:12223269]. There are at least twelve structural families of lectins:
- C-type lectins, which are Ca+-dependent.
- S-type (galectins), a widespread family of glycan-binding proteins [PUBMED:17497244].
- I-type, which have an immunoglobulin-like fold and can recognise sialic acids, other sugars and glycosaminoglycans [PUBMED:12223277].
- P-type, which bind phosphomannosyl receptors [PUBMED:12223278].
- Pentraxins [PUBMED:16343883].
- (Trout) egg lectins.
- Calreticulin and calnexin, which act as molecular chaperones of the endoplasmic reticulum [PUBMED:17072021].
- ERGIC-53 and VIP-36 [PUBMED:7876089].
- Discoidins [PUBMED:17702679].
- Eel aggutinins (fucolectins) [PUBMED:10924498].
- Annexin lectins [PUBMED:15813707].
- Fibrinogen-type lectins, which includes ficolins, tachylectins 5A and 5B, and Limax flavus (Spotted garden slug) agglutinin (these proteins have clear distinctions from one another, but they share a homologous fibrinogen-like domain used for carbohydrate binding).
- Also unclassified orphan lectins, including amphoterin, Cel-II, complement factor H, thrombospondin, sailic acid-binding lectins, adherence lectin, and cytokins (such as tumour necrosis factor and several interleukins).
C-type lectins can be further divided into seven subgroups based on additional non-lectin domains and gene structure: (I) hyalectans, (II) asialoglycoprotein receptors, (III) collectins, (IV) selectins, (V) NK group transmembrane receptors, (VI) macrophage mannose receptors, and (VII) simple (single domain) lectins [PUBMED:15476922].
Therefore, lectins are a diverse group of proteins, both in terms of structure and activity. Carbohydrate binding ability may have evolved independently and sporadically in numerous unrelated families, where each evolved a structure that was conserved to fulfil some other activity and function. In general, animal lectins act as recognition molecules within the immune system, their functions involving defence against pathogens, cell trafficking, immune regulation and the prevention of autoimmunity [PUBMED:14519388].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This clan contains domains that have a C-type lectin fold. Many of these are known or expected to mediate interactions with sugars.
The clan contains the following 11 members:APT C4 Chordopox_A33R DUF5075 Endostatin FGE-sulfatase Intimin_C Lectin_C Ly49 UL45 Xlink
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Author:||Sonnhammer ELL, Griffiths-Jones SR, Eberhardt R|
|Number in seed:||57|
|Number in full:||14082|
|Average length of the domain:||107.80 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||29.46 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There are 17 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Lectin_C domain has been found. There are 757 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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