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49  structures 567  species 0  interactions 4817  sequences 161  architectures

Family: zf-CW (PF07496)

Summary: CW-type Zinc Finger

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

CW-type Zinc Finger Provide feedback

This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by [1] and is predicted to be a "highly specialised mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including ...chromatin methylation status and early embryonic development." Weak homology to PF00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteristic of vertebrates, higher plants and other animals in which these domain is found [1].

Literature references

  1. Perry J, Zhao Y; , Trends Biochem Sci 2003;28:576-580.: The CW domain, a structural module shared amongst vertebrates, vertebrate-infecting parasites and higher plants. PUBMED:14607086 EPMC:14607086


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011124

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [ PUBMED:10529348 , PUBMED:15963892 , PUBMED:15718139 , PUBMED:17210253 , PUBMED:12665246 ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [ PUBMED:11179890 ]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants [ PUBMED:14607086 ].

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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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(152)
Full
(4817)
Representative proteomes UniProt
(8795)
RP15
(649)
RP35
(2238)
RP55
(4005)
RP75
(5423)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(152)
Full
(4817)
Representative proteomes UniProt
(8795)
RP15
(649)
RP35
(2238)
RP55
(4005)
RP75
(5423)
Alignment:
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Sequence:
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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
(152)
Full
(4817)
Representative proteomes UniProt
(8795)
RP15
(649)
RP35
(2238)
RP55
(4005)
RP75
(5423)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Yeats C
Number in seed: 152
Number in full: 4817
Average length of the domain: 47.20 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 5.31 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.5 27.5
Trusted cut-off 27.5 27.5
Noise cut-off 27.4 27.4
Model length: 48
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 adjacent tab. More...

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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 zf-CW domain has been found. There are 49 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096MIX0 View 3D Structure Click here
A0A096MK24 View 3D Structure Click here
A0A0G2JWF7 View 3D Structure Click here
A0A0G2K432 View 3D Structure Click here
A0A0P0VK92 View 3D Structure Click here
A0A0P0X9Z7 View 3D Structure Click here
A0A0R0F1Y3 View 3D Structure Click here
A0A0R0GCB3 View 3D Structure Click here
A0A0R0HXA8 View 3D Structure Click here
A0A0R0K8G3 View 3D Structure Click here
A0A0R0LBF6 View 3D Structure Click here
A0A0R4ITL2 View 3D Structure Click here
A0A1D6ESG6 View 3D Structure Click here
A0A1D6EY69 View 3D Structure Click here
A0A1D6F3Z3 View 3D Structure Click here
A0A1D6F4F1 View 3D Structure Click here
A0A1D6FRE1 View 3D Structure Click here
A0A1D6G4K5 View 3D Structure Click here
A0A1D6HAE6 View 3D Structure Click here
A0A1D6I7F9 View 3D Structure Click here
A0A1D6IFN3 View 3D Structure Click here
A0A1D6IND9 View 3D Structure Click here
A0A1D6K2Y1 View 3D Structure Click here
A0A1D6M447 View 3D Structure Click here
A0A1D6N125 View 3D Structure Click here
A3BF50 View 3D Structure Click here
A4I8X5 View 3D Structure Click here
B8A4L4 View 3D Structure Click here
C0P3Q8 View 3D Structure Click here
C6TGT6 View 3D Structure Click here
D3ZKF3 View 3D Structure Click here
D3ZP89 View 3D Structure Click here
D4A8J3 View 3D Structure Click here
F1LT90 View 3D Structure Click here
F1M2K1 View 3D Structure Click here
F1QGA2 View 3D Structure Click here
F4IZK5 View 3D Structure Click here
F7BJB9 View 3D Structure Click here
I1KJW5 View 3D Structure Click here
I1LLD5 View 3D Structure Click here
I1M2C3 View 3D Structure Click here
I1MEA8 View 3D Structure Click here
K7K117 View 3D Structure Click here
K7K3M0 View 3D Structure Click here
K7KCN0 View 3D Structure Click here
K7KG93 View 3D Structure Click here
K7KM54 View 3D Structure Click here
K7KUK4 View 3D Structure Click here
K7L3Q3 View 3D Structure Click here
K7LBT8 View 3D Structure Click here
K7LR55 View 3D Structure Click here
K7MJL6 View 3D Structure Click here
K7MQ27 View 3D Structure Click here
M0RC55 View 3D Structure Click here
Q08EN7 View 3D Structure Click here
Q0D5G4 View 3D Structure Click here
Q0DIA3 View 3D Structure Click here
Q0DIA4 View 3D Structure Click here
Q0DIQ5 View 3D Structure Click here
Q0DRX6 View 3D Structure Click here
Q0J0K9 View 3D Structure Click here
Q14149 View 3D Structure Click here
Q2LAE1 View 3D Structure Click here
Q4DPB2 View 3D Structure Click here
Q504Y3 View 3D Structure Click here
Q5CCK4 View 3D Structure Click here
Q5JL01 View 3D Structure Click here
Q5XEN5 View 3D Structure Click here
Q68EG7 View 3D Structure Click here
Q69XV8 View 3D Structure Click here
Q69ZX6 View 3D Structure Click here
Q6IR42 View 3D Structure Click here
Q6Z3U3 View 3D Structure Click here
Q86VD1 View 3D Structure Click here
Q8BMD7 View 3D Structure Click here
Q8C5W4 View 3D Structure Click here
Q8CIG3 View 3D Structure Click here
Q8GY51 View 3D Structure Click here
Q8LA53 View 3D Structure Click here
Q8NB78 View 3D Structure Click here
Q8TE76 View 3D Structure Click here
Q8W4L5 View 3D Structure Click here
Q94IR1 View 3D Structure Click here
Q9FZP6 View 3D Structure Click here
Q9H0M4 View 3D Structure Click here
Q9LYB9 View 3D Structure Click here
Q9M1I1 View 3D Structure Click here
Q9WVL5 View 3D Structure Click here
Q9Y6X9 View 3D Structure Click here