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102  structures 1585  species 0  interactions 49585  sequences 1112  architectures

Family: zf-CCCH (PF00642)

Summary: Zinc finger C-x8-C-x5-C-x3-H type (and similar)

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Zinc finger C-x8-C-x5-C-x3-H type (and similar) Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000571

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 C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [ PUBMED:9703499 , PUBMED:10330172 ]. This type of Znf is very often present in two copies.

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 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


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.

Representative proteomes UniProt
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PP/heatmap 1            

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

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

Format an alignment

Representative proteomes UniProt

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.

Representative proteomes UniProt
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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...


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: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 70
Number in full: 49585
Average length of the domain: 26.3 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 7.47 %

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 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 27
Family (HMM) version: 27
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


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


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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 domain has been found. There are 102 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
A0A044QYQ5 View 3D Structure Click here
A0A044R230 View 3D Structure Click here
A0A044RHV1 View 3D Structure Click here
A0A044RHV6 View 3D Structure Click here
A0A044RHW9 View 3D Structure Click here
A0A044RSP0 View 3D Structure Click here
A0A044S5J1 View 3D Structure Click here
A0A044S5L3 View 3D Structure Click here
A0A044S5M2 View 3D Structure Click here
A0A044S5M7 View 3D Structure Click here
A0A044SQV0 View 3D Structure Click here
A0A044T1H4 View 3D Structure Click here
A0A044UL03 View 3D Structure Click here
A0A044UMK6 View 3D Structure Click here
A0A044UP17 View 3D Structure Click here
A0A044UPV6 View 3D Structure Click here
A0A044V0X3 View 3D Structure Click here
A0A044V537 View 3D Structure Click here
A0A077YWY2 View 3D Structure Click here
A0A077Z444 View 3D Structure Click here
A0A077Z6W1 View 3D Structure Click here
A0A077ZCN9 View 3D Structure Click here
A0A077ZJG9 View 3D Structure Click here
A0A096Q3U9 View 3D Structure Click here
A0A096T535 View 3D Structure Click here
A0A0A2UYQ7 View 3D Structure Click here
A0A0D2DFK9 View 3D Structure Click here
A0A0D2E2G4 View 3D Structure Click here
A0A0D2F9G8 View 3D Structure Click here
A0A0D2F9Q1 View 3D Structure Click here
A0A0D2FDU0 View 3D Structure Click here
A0A0D2G629 View 3D Structure Click here
A0A0D2H5N4 View 3D Structure Click here
A0A0D2HFJ0 View 3D Structure Click here
A0A0G2JVM3 View 3D Structure Click here
A0A0G2JX72 View 3D Structure Click here
A0A0G2JZE8 View 3D Structure Click here
A0A0G2JZH9 View 3D Structure Click here
A0A0G2K214 View 3D Structure Click here
A0A0H5S2Q9 View 3D Structure Click here