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4  structures 1355  species 0  interactions 7849  sequences 485  architectures

Family: zf-CCCH_4 (PF18044)

Summary: CCCH-type zinc finger

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

CCCH-type zinc finger Provide feedback

This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR041367

This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.

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 CCCH_zf (CL0537), which has the following description:

This superfamily is characterised by families of proteins with several Cys3His zinc-binding domains in tandem.

The clan contains the following 11 members:

Nab2p_Zf1 Torus zf-CCCH zf-CCCH_2 zf-CCCH_3 zf-CCCH_4 zf-CCCH_6 zf-CCCH_7 zf-CCCH_8 zf_CCCH_4 zf_CCCH_5

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...

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
(16)
Full
(7849)
Representative proteomes UniProt
(12721)
RP15
(1140)
RP35
(3171)
RP55
(5990)
RP75
(8146)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(16)
Full
(7849)
Representative proteomes UniProt
(12721)
RP15
(1140)
RP35
(3171)
RP55
(5990)
RP75
(8146)
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
(16)
Full
(7849)
Representative proteomes UniProt
(12721)
RP15
(1140)
RP35
(3171)
RP55
(5990)
RP75
(8146)
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: ECOD:EUF06031
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 16
Number in full: 7849
Average length of the domain: 22.10 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 4.10 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.6 24.6
Trusted cut-off 24.6 24.6
Noise cut-off 24.5 24.5
Model length: 22
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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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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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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-CCCH_4 domain has been found. There are 4 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
A0A0G2QC40 View 3D Structure Click here
A0A0R0IMJ3 View 3D Structure Click here
A0A0R4IIP1 View 3D Structure Click here
A0A1D6HFW3 View 3D Structure Click here
A0A1D6HIE7 View 3D Structure Click here
A0A1D6NZP1 View 3D Structure Click here
A0A2R8Q3V8 View 3D Structure Click here
A1Z7R9 View 3D Structure Click here
A4I2T3 View 3D Structure Click here
A9C4A6 View 3D Structure Click here
B4FAY0 View 3D Structure Click here
B4FE66 View 3D Structure Click here
D3ZQV3 View 3D Structure Click here
D3ZVW3 View 3D Structure Click here
D3ZY41 View 3D Structure Click here
E0X9N4 View 3D Structure Click here
E7FGZ9 View 3D Structure Click here
F1QCB1 View 3D Structure Click here
I1J6A5 View 3D Structure Click here
I1K1F1 View 3D Structure Click here
I1KBI1 View 3D Structure Click here
I1KYC3 View 3D Structure Click here
I1MJM5 View 3D Structure Click here
I1N0J9 View 3D Structure Click here
K7KEY3 View 3D Structure Click here
K7KLH6 View 3D Structure Click here
K7M8D9 View 3D Structure Click here
K7MEJ2 View 3D Structure Click here
K7ML63 View 3D Structure Click here
K7MYD7 View 3D Structure Click here
K7TI82 View 3D Structure Click here
K7UB91 View 3D Structure Click here
O74463 View 3D Structure Click here
O82307 View 3D Structure Click here
P34366 View 3D Structure Click here
P41000 View 3D Structure Click here
Q02799 View 3D Structure Click here
Q0DYP5 View 3D Structure Click here
Q0P678 View 3D Structure Click here
Q13064 View 3D Structure Click here