Summary: Calponin homology (CH) domain

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Wikipedia: Calponin homology domain
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Calponin homology domain Edit Wikipedia article

Calponin homology (CH) domain

Solution structure of calponin homology domain of IQGAP1^[1]

Identifiers

Symbol

CH

1aoa / SUPFAM

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary
PDB	1sjjB:33-136 1tjtA:46-149 1wkuA:46-149 1sh5B:186-293 1sh6A:186-293 1mb8A:180-282 1dxxA:16-119 1qagB:32-135 1rt8A:386-495 1pxyB:393-498 1aoa :121-236 1wypA:29-132 1h67A:29-132 1wynA:29-132 1ujoA:25-138 1wymA:25-137 1wyrA:4-111 1p2xA:42-148 1p5sA:42-148 1bkrA:174-278 1aa2 :174-278 1wyqA:178-281 1bhdA:151-254 1wylA:509-612 1wjoA:517-624 1wyoA:15-116 1vkaB:15-116 1uegA:15-116 1pa7A:15-116

Calponin homology domain (or CH domain) is a family of actin binding domains found in both cytoskeletal proteins and signal transduction proteins.^[2] The domain is about 100 amino acids in length and is composed of four alpha helices.^[3] It comprises the following groups of actin-binding domains:

Actinin-type (including spectrin, fimbrin, ABP-280)
Calponin-type

A comprehensive review of proteins containing this type of actin-binding domains is given in.^[4]

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.^[5] 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 been determined using X-ray crystallography.^[6]

Examples

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

References

^ 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. CiteSeerX 10.1.1.608.8653. 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.

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

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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

Castresana J, Saraste M; , FEBS Lett 1995;374:149-151.: Does Vav bind to F-actin through a CH domain? PUBMED:7589522 EPMC:7589522
Carugo KD, Banuelos S, Saraste M; , Nat Struct Biol 1997;4:175-179.: Crystal structure of a calponin homology domain. PUBMED:9164454 EPMC:9164454
Stradal T, Kranewitter W, Winder SJ, Gimona M; , FEBS Lett 1998;431:134-137.: CH domains revisited. PUBMED:9708889 EPMC:9708889
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

Internal database links

SCOOP:	CAMSAP_CH CDC24 CH_2 HOOK
Similarity to PfamA using HHSearch:	CH_2 CAMSAP_CH

External database links

HOMSTRAD:	CH
PROSITE:	PDOC00019
SCOP:	1aoa
SMART:	CH

This tab holds annotation information from the InterPro database.

InterPro entry IPR001715

A number of actin-binding proteins, including spectrin, alpha-actinin and fimbrin, contain a 250 amino acid stretch called the actin binding domain (ABD). The ABD has probably arisen from duplication of a domain which is also found in a single copy in a number of other proteins like calponin or the vav proto-oncogene and has been called calponin homology (CH) domain [PUBMED:9708889, PUBMED:9887274].

A detailed analysis of The CH domain-containing proteins has shown that they can be divided in three groups [PUBMED:9708889]:

The fimbrin family of monomeric actin cross-linking molecules containing two ABDs
Dimeric cross-linking proteins (alpha-actinin, beta-spectrin, filamin, etc.) and monomeric F-actin binding proteins (dystrophin, utrophin) each containing one ABD
Proteins containing only a single amino terminal CH domain.

Each single ABD, comprising two CH domains, is able to bind one actin monomer in the filament. The amino terminal CH domain has the intrinsic ability to bind actin, albeit with lower affinity than the complete ABD, whereas the carboxy terminal CH bind actin extremely weakly or not at all. Nevertheless both CH domains are required for a fully functional ABD; the C-terminal CH domain contributing to the overall stability of the complete ABD through inter-domain helix-helix interactions [PUBMED:9708889]. Some of the proteins containing a single CH domain also bind to actin, although this has not been shown to be via the single CH domain alone [PUBMED:9887274]. In addition, the CH domain occurs also in a number of proteins not known to bind actin, a notable example being the vav protooncogene.

The resolution of the 3D structure of various CH domains has shown that the conserved core consist of four major alpha-helices [PUBMED:9887274].

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].

Gene Ontology

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)

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 6 members:

CAMSAP_CH CDC24 CH CH_2 IFT81_CH MIP-T3

Alignments

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RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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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 (122)	Full (32767)	Representative proteomes				UniProt (50124)	NCBI (99783)	Meta (49)
	Seed (122)	Full (32767)	RP15 (7060)	RP35 (14272)	RP55 (22151)	RP75 (26550)	UniProt (50124)	NCBI (99783)	Meta (49)
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HTML	View
PP/heatmap	₁

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (122)	Full (32767)	Representative proteomes				UniProt (50124)	NCBI (99783)	Meta (49)
	Seed (122)	Full (32767)	RP15 (7060)	RP35 (14272)	RP55 (22151)	RP75 (26550)	UniProt (50124)	NCBI (99783)	Meta (49)
Alignment:
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Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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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 (122)	Full (32767)	Representative proteomes				UniProt (50124)	NCBI (99783)	Meta (49)
	Seed (122)	Full (32767)	RP15 (7060)	RP35 (14272)	RP55 (22151)	RP75 (26550)	UniProt (50124)	NCBI (99783)	Meta (49)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download	Download

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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.

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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

Seed source:

Prosite

Previous IDs:

actinin-binding;

Type:

Domain

Sequence Ontology:

SO:0000417

Author:

Finn RD

Number in seed:

122

Number in full:

32767

Average length of the domain:

107.50 aa

Average identity of full alignment:

19 %

Average coverage of the sequence by the domain:

11.49 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	26.0	22.1
Trusted cut-off	26.0	22.1
Noise cut-off	25.9	22.0

Model length:

109

Family (HMM) version:

31

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Species distribution

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Unmapped species names

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Interactive tree

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.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

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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Interactions

There are 14 interactions for this family. More...

Actin EFhand_Ca_insen Paxillin CH Pkinase_Tyr EF-hand_1 EF-hand_7 Spectrin PH RhoGEF Tubulin_C Tubulin EFhand_Ca_insen fn3

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 222 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 sequence.

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Family: CH (PF00307)

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