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61  structures 403  species 1  interaction 2431  sequences 42  architectures

Family: Cofilin_ADF (PF00241)

Summary: Cofilin/tropomyosin-type actin-binding protein

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This is the Wikipedia entry entitled "ADF-H domain". More...

ADF-H domain Edit Wikipedia article

Cofilin_ADF
PDB 1f7s EBI.jpg
crystal structure of adf1 from arabidopsis thaliana
Identifiers
Symbol Cofilin_ADF
Pfam PF00241
Pfam clan CL0092
InterPro IPR002108
SMART ADF
PROSITE PDOC00297
SCOP 2prf
SUPERFAMILY 2prf
CDD cd00013

In molecular biology, ADF-H domain (actin-depolymerising factor homology domain) is an approximately 150 amino acid motif that is present in three phylogenetically distinct classes of eukaryotic actin-binding proteins.[1][2][3]

  • Twinfilins, which are actin monomer-binding proteins that are composed of two ADF-H domains
  • Abp1/Drebrins, which are relatively large proteins composed of an N-terminal ADF-H domain followed by a variable region and a C-terminal SH3 domain. Abp1/Drebrins interact only with actin filaments and do not promote filament depolymerisation or fragmentation Although these proteins are biochemically distinct and play different roles in actin dynamics, they all appear to use the ADF-H domain for their interactions with actin.

The ADF-H domain consists of a six-stranded mixed beta-sheet in which the four central strands (beta2-beta5) are anti-parallel and the two edge strands (beta1 and beta6) run parallel with the neighbouring strands. The sheet is surrounded by two alpha-helices on each side .[1][2][4]

References[edit]

  1. ^ a b Lappalainen P, Kessels MM, Cope MJ, Drubin DG (August 1998). "The ADF homology (ADF-H) domain: a highly exploited actin-binding module". Mol. Biol. Cell 9 (8): 1951–9. PMC 25446. PMID 9693358. 
  2. ^ a b Paavilainen VO, Merckel MC, Falck S, Ojala PJ, Pohl E, Wilmanns M, Lappalainen P (November 2002). "Structural conservation between the actin monomer-binding sites of twinfilin and actin-depolymerizing factor (ADF)/cofilin". J. Biol. Chem. 277 (45): 43089–95. doi:10.1074/jbc.M208225200. PMID 12207032. 
  3. ^ Liu LX, Xu H, Weller PF, Shi A, Debnath I (February 1997). "Structure and expression of a novel filarial gene for glia maturation factor". Gene 186 (1): 1–5. doi:10.1016/S0378-1119(96)00585-9. PMID 9047337. 
  4. ^ Liu L, Wei Z, Wang Y, Wan M, Cheng Z, Gong W (November 2004). "Crystal structure of human coactosin-like protein". J. Mol. Biol. 344 (2): 317–23. doi:10.1016/j.jmb.2004.09.036. PMID 15522287. 

This article incorporates text from the public domain Pfam and InterPro IPR002108

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.

Cofilin/tropomyosin-type actin-binding protein Provide feedback

Severs actin filaments and binds to actin monomers.

Literature references

  1. Fedorov AA, Lappalainen P, Fedorov EV, Drubin DG, Almo SC; , Nat Struct Biol 1997;4:366-369.: Structure determination of yeast cofilin. PUBMED:9145106 EPMC:9145106

  2. Leonard SA, Gittis AG, Petrella EC, Pollard TD, Lattman EE; , Nat Struct Biol 1997;4:369-373.: Crystal structure of the actin-binding protein actophorin from Acanthamoeba. PUBMED:9145107 EPMC:9145107

  3. Jiang CJ, Weeds AG, Khan S, Hussey PJ; , Proc Natl Acad Sci U S A 1997;94:9973-9978.: F-actin and G-actin binding are uncoupled by mutation of conserved tyrosine residues in maize actin depolymerizing factor. PUBMED:9275236 EPMC:9275236

  4. Lappalainen P, Drubin DG; , Nature 1997;388:78-82.: Cofilin promotes rapid actin filament turnover in vivo. PUBMED:9214506 EPMC:9214506


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002108

The actin-depolymerising factor homology (ADF-H) domain is an ~150-amino acid motif that is present in three phylogenetically distinct classes of eukaryotic actin-binding proteins [PUBMED:9693358, PUBMED:12207032, PUBMED:9047337]:

  • ADF/cofilins, which include ADF, cofilin, destrin, actophorin, coactosin, depactin and glia maturation factors (GMFs) beta and gamma. ADF/cofilins are small actin-binding proteins composed of a single ADF-H domain. They bind both actin-monomers and filaments and promote rapid filament turnover in cells by depolymerising/fragmenting actin filaments. ADF/cofilins bind ADP-actin with higher affinity than ATP-actin and inhibit the spontaneous nucleotide exchange on actin monomers
  • Twinfilins, which are actin monomer-binding proteins that are composed of two ADF-H domains
  • Abp1/Drebrins, which are relatively large proteins composed of an N-terminal ADF-H domain followed by a variable region and a C-terminal SH3 domain. Abp1/Drebrins interact only with actin filaments and do not promote filament depolymerisation or fragmentation

Although these proteins are biochemically distinct and play different roles in actin dynamics, they all appear to use the ADF-H domain for their interactions with actin.

The ADF-H domain consists of a six-stranded mixed beta-sheet in which the four central strands (beta2-beta5) are anti-parallel and the two edge strands (beta1 and beta6) run parallel with the neighbouring strands. The sheet is surrounded by two alpha-helices on each side [PUBMED:9693358, PUBMED:12207032, PUBMED:15522287].

Gene Ontology

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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 ADF (CL0092), which has the following description:

For motile cells such as Amoeba to move, there must be the rapid recycling of their actin cytoskeleton to enable a dynamic change in their shape. Gelsolin (PFAM:PF00626) and Cofilin (PFAM:PF00241) are two key domain families in this process. Both of these domain are structural and functional similar [1,2]. In particular, the beta sheet found at the core of the domain is structurally well conserved, with the helices that surround this sheet less conserved[2].

The clan contains the following 2 members:

Cofilin_ADF Gelsolin

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
(16)
Full
(2431)
Representative proteomes NCBI
(2235)
Meta
(7)
RP15
(449)
RP35
(733)
RP55
(1114)
RP75
(1450)
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  Seed
(16)
Full
(2431)
Representative proteomes NCBI
(2235)
Meta
(7)
RP15
(449)
RP35
(733)
RP55
(1114)
RP75
(1450)
Alignment:
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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
(16)
Full
(2431)
Representative proteomes NCBI
(2235)
Meta
(7)
RP15
(449)
RP35
(733)
RP55
(1114)
RP75
(1450)
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.

Pfam alignments:

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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.

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; SMART;
Previous IDs: cofilin_ADF;
Type: Domain
Author: Chris Ponting, Joerg Schultz, Peer Bork, Finn RD
Number in seed: 16
Number in full: 2431
Average length of the domain: 121.70 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 53.52 %

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 21.1 21.1
Trusted cut-off 21.2 21.1
Noise cut-off 21.0 20.9
Model length: 127
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Cofilin_ADF

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 Cofilin_ADF domain has been found. There are 61 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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