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152  structures 496  species 2  interactions 10780  sequences 564  architectures

Family: CH (PF00307)

Summary: Calponin homology (CH) domain

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This is the Wikipedia entry entitled "Calponin homology domain". More...

Calponin homology domain Edit Wikipedia article

Calponin homology (CH) domain
2RR8.pdb.jpg
Solution structure of calponin homology domain of IQGAP1[1]
Identifiers
Symbol CH
Pfam PF00307
InterPro IPR001715
SMART CH
PROSITE PDOC00019
SCOP 1aoa
SUPERFAMILY 1aoa

Calponin homology actin-binding domain (or CH domain) is a superfamily of actin binding domains found in both cytoskeletal proteins and signal transduction proteins.[2] It comprises the following groups of actin-binding domains:

A comprehensive review of proteins containing this type of actin-binding domains is given in.[3]

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.[4] Most proteins have two copies of the CH domain, however some proteins such as calponin and the human vav proto-oncogene (P15498) have only a single copy. The structure of an example CH-domain has recently been solved.[5]

Examples

Human genes encoding calponin homology domain-containing proteins include:

References

  1. ^ 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): 59–64. doi:10.1007/s10858-010-9434-8. PMID 20644981. 
  2. ^ Saraste M, Castresana J (1995). "Does Vav bind to F-actin through a CH domain?". FEBS Lett. 374 (2): 149–151. doi:10.1016/0014-5793(95)01098-Y. PMID 7589522. 
  3. ^ Hartwig JH (1995). "Actin-binding proteins. 1: Spectrin super family". Protein Prof. 2 (7): 703–800. PMID 7584474. 
  4. ^ Gimona M, Mital R (1998). "The single CH domain of calponin is neither sufficient nor necessary for F-actin binding". J. Cell Sci. 111: 1813–1821. PMID 9625744. 
  5. ^ Saraste M, Carugo KD, Banuelos S (1997). "Crystal structure of a calponin homology domain". Nat. Struct. Biol. 4 (3): 175–179. doi:10.1038/nsb0397-175. PMID 9164454. 

This article incorporates text from the public domain Pfam and InterPro IPR001715


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.

Calponin homology (CH) domain Provide feedback

The CH domain is found in both cytoskeletal proteins and signal transduction proteins [1]. 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 [4]. 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.

Literature references

  1. Castresana J, Saraste M; , FEBS Lett 1995;374:149-151.: Does Vav bind to F-actin through a CH domain? PUBMED:7589522 EPMC:7589522

  2. Carugo KD, Banuelos S, Saraste M; , Nat Struct Biol 1997;4:175-179.: Crystal structure of a calponin homology domain. PUBMED:9164454 EPMC:9164454

  3. Stradal T, Kranewitter W, Winder SJ, Gimona M; , FEBS Lett 1998;431:134-137.: CH domains revisited. PUBMED:9708889 EPMC:9708889

  4. Gimona M, Mital R; , J Cell Sci 1998;111:1813-1821.: The single CH domain of calponin is neither sufficient nor necessary for F-actin binding. PUBMED:9625744 EPMC:9625744


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:

  • Actinin-type (including spectrin, fimbrin, ABP-280) (see INTERPRO).
  • Calponin-type (see INTERPRO).

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 its 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].

This entry represents the calponin-homology (CH) domain, a superfamily of actin-binding domains found in cytoskeletal proteins (contain two CH domain in tandem repeat), in regulatory proteins from muscle, and in signal transduction proteins. This domain has a core structure consisting of a 4-helical bundle. This domain is found in:

  • 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].

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 CH (CL0188), which has the following description:

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 [1].

The clan contains the following 4 members:

CAMSAP_CH CDC24 CH DUF1042

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...

View options

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
(194)
Full
(10780)
Representative proteomes NCBI
(10465)
Meta
(47)
RP15
(1688)
RP35
(2487)
RP55
(4051)
RP75
(5898)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(194)
Full
(10780)
Representative proteomes NCBI
(10465)
Meta
(47)
RP15
(1688)
RP35
(2487)
RP55
(4051)
RP75
(5898)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(194)
Full
(10780)
Representative proteomes NCBI
(10465)
Meta
(47)
RP15
(1688)
RP35
(2487)
RP55
(4051)
RP75
(5898)
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: Prosite
Previous IDs: actinin-binding;
Type: Domain
Author: Finn RD
Number in seed: 194
Number in full: 10780
Average length of the domain: 104.80 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 12.85 %

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 22.1 22.1
Trusted cut-off 22.1 22.1
Noise cut-off 22.0 22.0
Model length: 108
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Actin CH

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 CH domain has been found. There are 152 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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