Summary: Calponin homology (CH) domain
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Calponin homology domain Edit Wikipedia article
|Calponin homology (CH) domain|
Solution structure of calponin homology domain of IQGAP1
Calponin homology domain (or CH domain) is a family of actin binding domains found in both cytoskeletal proteins and signal transduction proteins. The domain is about 100 amino acids in length and is composed of four alpha helices. It comprises the following groups of actin-binding domains:
A comprehensive review of proteins containing this type of actin-binding domains is given in.
The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most proteins have two copies of the CH domain, however some proteins such as calponin and the human vav proto-oncogene ( ) have only a single copy. The structure of an example CH domain has been determined using X-ray crystallography.
Human genes encoding calponin homology domain-containing proteins include:
- ACTN1, ACTN2, ACTN3, ACTN4, ARHGEF6, ARHGEF7, ASPM,
- CLMN, CNN1, CNN2, CNN3,
- DIXDC1, DMD, DST,
- EHBP1, EHBP1L1,
- FLNA, FLNB, FLNC,
- GAS2, GAS2L1, GAS2L2, GAS2L3,
- IQGAP1, IQGAP2, IQGAP3,
- LCP1, LIMCH1, LMO7, LRCH1, LRCH2, LRCH3, LRCH4,
- MACF1, MAPRE1, MAPRE2, MAPRE3, MICAL1, MICAL2, MICAL2PV1, MICAL2PV2, MICAL3, MICALL1, MICALL2,
- NAV2, NAV3,
- PARVA, PARVB, PARVG, PLEC1, PLS1, PLS3, PP14183,
- SMTN, SMTNL2, SPECC1, SPECC1L, SPNB4, SPTB, SPTBN1, SPTBN2, SPTBN4, SPTBN5, SYNE1, SYNE2,
- TAGLN, TAGLN2, TAGLN3,
- UTRN, and
- VAV1, VAV2, VAV3
- PDB 2RR8; Umemoto R, Nishida N, Ogino S, Shimada I (September 2010). "NMR structure of the calponin homology domain of human IQGAP1 and its implications for the actin recognition mode". J. Biomol. NMR 48 (1): 59â€“64. doi:10.1007/s10858-010-9434-8. PMID 20644981.
- Saraste M, Castresana J (1995). "Does Vav bind to F-actin through a CH domain?". FEBS Lett. 374 (2): 149â€“151. doi:10.1016/0014-5793(95)01098-Y. PMID 7589522.
- Korenbaum, E.; Rivero, F. (Sep 2002). "Calponin homology domains at a glance.". J Cell Sci 115 (Pt 18): 3543â€“5. doi:10.1242/jcs.00003. PMID 12186940.
- Hartwig JH (1995). "Actin-binding proteins. 1: Spectrin super family". Protein Prof. 2 (7): 703â€“800. PMID 7584474.
- Gimona M, Mital R (1998). "The single CH domain of calponin is neither sufficient nor necessary for F-actin binding". J. Cell Sci. 111: 1813â€“1821. PMID 9625744.
- Saraste M, Carugo KD, Banuelos S (1997). "Crystal structure of a calponin homology domain". Nat. Struct. Biol. 4 (3): 175â€“179. doi:10.1038/nsb0397-175. PMID 9164454.
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Calponin homology (CH) domain Provide feedback
The CH domain is found in both cytoskeletal proteins and signal transduction proteins . The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity . Most member proteins have from two to four copies of the CH domain, however some proteins such as calponin and P15498 have only a single copy.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001715
The calponin homology domain (also known as CH-domain) is a superfamily of actin-binding domains found in both cytoskeletal proteins and signal transduction proteins [PUBMED:7589522]. It comprises the following groups of actin-binding domains:
A comprehensive review of proteins containing this type of actin-binding domains is given in [PUBMED:7584474].
The CH domain is involved in actin binding in some members of the family. However, in calponins there is evidence that the CH domain is not involved in their actin binding activity [PUBMED:9625744]. Most proteins have two copies of the CH domain, however some proteins such as calponin and the human vav proto-oncogene (SWISSPROT) have only a single copy. The structure of an example CH-domain has recently been solved [PUBMED:9164454].
Proteins containing a calponin domain include:
- Calponin, which is involved in the regulation of contractility and organisation of the actin cytoskeleton in smooth muscle cells [PUBMED:11839310].
- Beta-spectrin, a major component of a submembrane cytoskeletal network connecting actin filaments to integral plasma membrane proteins [PUBMED:17121810].
- The actin-cross-linking domain of the fimbrin/plastin family of actin filament bundling or cross-linking proteins [PUBMED:9302997].
- Utrophin,a close homologue of dystrophin [PUBMED:9887274].
- Dystrophin, the protein found to be defective in Duchenne muscular dystrophy; this protein contains a tandem repeat of two CH domains [PUBMED:10801490].
- Actin-binding domain of plectin, a large and widely expressed cytolinker protein [PUBMED:15128297].
- The N-terminal microtubule-binding domain of microtubule-associated protein eb1 (end-binding protein), a member of a conserved family of proteins that localise to the plus-ends of microtubules [PUBMED:12857735].
- Ras GTPase-activating-like protein rng2, an IQGAP protein that is essential for the assembly of an actomyosin ring during cytokinesis [PUBMED:15272162].
- Transgelin, which suppresses androgen receptor transactivation [PUBMED:17082327].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||protein binding (GO:0005515)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
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The calponin homology (CH) domain is found in a variety of contexts, ranging from proteins involved in signalling pathways to cytoskeletal proteins. They seem to have diverse cellular functions, which are thought to include actin binding, involvement in the MAP kinase signalling pathway, and regulation of GEF activity in Rho family GTPase pathways. Structurally, they are organised into three layers, with two parallel alpha helices in the core being sandwiched between another two helices, one on each side .
The clan contains the following 4 members:CAMSAP_CH CDC24 CH CH_2
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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|Number in seed:||131|
|Number in full:||16562|
|Average length of the domain:||102.10 aa|
|Average identity of full alignment:||19 %|
|Average coverage of the sequence by the domain:||13.06 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||27|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
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How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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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 14 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 CH domain has been found. There are 184 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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