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504  structures 521  species 7  interactions 12227  sequences 665  architectures

Family: Lectin_C (PF00059)

Summary: Lectin C-type domain

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This is the Wikipedia entry entitled "C-type lectin". More...

C-type lectin Edit Wikipedia article

Lectin C-type domain
PDB 1jzn EBI.jpg
Pentameric structure of rattlesnake venom lectin which is a galactose binding lectin.[1]
Identifiers
Symbol Lectin_C
Pfam PF00059
InterPro IPR001304
SMART CLECT
PROSITE PS50041
SCOP 2msb
SUPERFAMILY 2msb

A C-type lectin (CLEC) is a type of carbohydrate-binding protein domain known as a lectin.[2] The C-type designation is from their requirement for calcium for binding.[3] Proteins that contain C-type lectin domains have a diverse range of functions including cell-cell adhesion, immune response to pathogens and apoptosis.[4][5]

Classification[edit]

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.[6] This classification was subsequently updated in 2002, leading to seven additional groups (VIII to XIV).[7] Most recently, three further subgroups were added (XV to XVII).[2]

Group Name Associated domains
I Lecticans EGF, Sushi, Ig and Link domains
II Asialoglycoprotein and DC receptors None
III Collectins None
IV Selectins Sushi and EGF domains
V NK - cell receptors None
VI Multi-CTLD endocytic receptors FnII and Ricin domains
VII Reg group None
VIII Chondrolectin, Layilin None
IX Tetranectin None
X Polycystin WSC, REJ, PKD domains
XI Attractin (ATRN) PSI, EGF and CUB domains
XII Eosinophil major basic protein (EMBP) None
XIII DGCR2 None
XIV Thrombomodulin EGF domains
XV Bimlec None
XVI SEEC SCP and EGF domains
XVII CBCP/Frem1/QBRICK CSPG repeats and CalX-beta domains

CLECs include:

The "NK Cell lectin-like receptors" are a very closely related group:[8]

Additional proteins containing this domain include:

References[edit]

  1. ^ 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. 
  2. ^ a b 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. 
  3. ^ C-Type Lectin at the US National Library of Medicine Medical Subject Headings (MeSH)
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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. 
  7. ^ Drickamer K, Fadden AJ (2002). "Genomic analysis of C-type lectins". Biochem. Soc. Symp. (69): 59–72. PMID 12655774. 
  8. ^ NK Cell Lectin-Like Receptors at the US National Library of Medicine Medical Subject Headings (MeSH)

External links[edit]

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.

Lectin C-type domain Provide feedback

This family includes both long and short form C-type

Literature references

  1. 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


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].

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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Pfam Clan

This family is a member of clan C_Lectin (CL0056), which has the following description:

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 7 members:

APT C4 Chordopox_A33R Herpes_UL45 Intimin_C Lectin_C Xlink

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
(95)
Full
(12227)
Representative proteomes NCBI
(11645)
Meta
(360)
RP15
(2294)
RP35
(3027)
RP55
(5110)
RP75
(7014)
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  Seed
(95)
Full
(12227)
Representative proteomes NCBI
(11645)
Meta
(360)
RP15
(2294)
RP35
(3027)
RP55
(5110)
RP75
(7014)
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
(95)
Full
(12227)
Representative proteomes NCBI
(11645)
Meta
(360)
RP15
(2294)
RP35
(3027)
RP55
(5110)
RP75
(7014)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: Swissprot_feature_table
Previous IDs: lectin_c;
Type: Domain
Author: Sonnhammer ELL, Griffiths-Jones SR, Eberhardt R
Number in seed: 95
Number in full: 12227
Average length of the domain: 107.50 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 30.77 %

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 105
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

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

fn3 Lectin_C EGF C1-set Surfac_D-trimer MHC_I VWA

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 Lectin_C domain has been found. There are 504 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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