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100  structures 1494  species 0  interactions 42872  sequences 1093  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

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
(70)
Full
(42872)
Representative proteomes UniProt
(78902)
RP15
(6478)
RP35
(19772)
RP55
(35023)
RP75
(47516)
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
(70)
Full
(42872)
Representative proteomes UniProt
(78902)
RP15
(6478)
RP35
(19772)
RP55
(35023)
RP75
(47516)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(70)
Full
(42872)
Representative proteomes UniProt
(78902)
RP15
(6478)
RP35
(19772)
RP55
(35023)
RP75
(47516)
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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 70
Number in full: 42872
Average length of the domain: 26.30 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 7.67 %

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 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 27
Family (HMM) version: 26
Download: download the raw HMM for this family

Species distribution

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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-CCCH domain has been found. There are 100 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
A0A096Q3U9 View 3D Structure Click here
A0A096T535 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
A0A0G2K214 View 3D Structure Click here
A0A0P0W5V0 View 3D Structure Click here
A0A0P0XPQ0 View 3D Structure Click here
A0A0R0EAY8 View 3D Structure Click here
A0A0R0G9I4 View 3D Structure Click here
A0A0R0G9I4 View 3D Structure Click here
A0A0R0G9I4 View 3D Structure Click here
A0A0R0G9I4 View 3D Structure Click here
A0A0R0G9I4 View 3D Structure Click here
A0A0R0H030 View 3D Structure Click here
A0A0R0HN52 View 3D Structure Click here
A0A0R0HN52 View 3D Structure Click here
A0A0R0HN52 View 3D Structure Click here
A0A0R0HN52 View 3D Structure Click here
A0A0R0HN52 View 3D Structure Click here
A0A0R0HZS3 View 3D Structure Click here
A0A0R0ITE7 View 3D Structure Click here
A0A0R0ITE7 View 3D Structure Click here
A0A0R4IBW1 View 3D Structure Click here
A0A0R4IBW1 View 3D Structure Click here
A0A0R4IY72 View 3D Structure Click here
A0A140UHW6 View 3D Structure Click here
A0A1D6EFY7 View 3D Structure Click here
A0A1D6EZ54 View 3D Structure Click here
A0A1D6FBY3 View 3D Structure Click here
A0A1D6FBY3 View 3D Structure Click here
A0A1D6FBY3 View 3D Structure Click here
A0A1D6FBY3 View 3D Structure Click here
A0A1D6FBY3 View 3D Structure Click here
A0A1D6FBZ0 View 3D Structure Click here
A0A1D6FBZ0 View 3D Structure Click here
A0A1D6FBZ0 View 3D Structure Click here
A0A1D6FBZ0 View 3D Structure Click here
A0A1D6FBZ0 View 3D Structure Click here
A0A1D6FV35 View 3D Structure Click here
A0A1D6FZC1 View 3D Structure Click here
A0A1D6FZC1 View 3D Structure Click here
A0A1D6FZC1 View 3D Structure Click here
A0A1D6FZC1 View 3D Structure Click here
A0A1D6FZC1 View 3D Structure Click here
A0A1D6G684 View 3D Structure Click here
A0A1D6G684 View 3D Structure Click here
A0A1D6G684 View 3D Structure Click here
A0A1D6G684 View 3D Structure Click here
A0A1D6GK17 View 3D Structure Click here
A0A1D6HAP5 View 3D Structure Click here
A0A1D6HAP5 View 3D Structure Click here
A0A1D6IML9 View 3D Structure Click here
A0A1D6IUH6 View 3D Structure Click here
A0A1D6IUH6 View 3D Structure Click here
A0A1D6IUH6 View 3D Structure Click here
A0A1D6J2R7 View 3D Structure Click here
A0A1D6K022 View 3D Structure Click here
A0A1D6K1Q4 View 3D Structure Click here
A0A1D6L005 View 3D Structure Click here
A0A1D6L005 View 3D Structure Click here
A0A1D6L005 View 3D Structure Click here
A0A1D6L005 View 3D Structure Click here
A0A1D6L005 View 3D Structure Click here
A0A1D6L005 View 3D Structure Click here
A0A1D6L0C8 View 3D Structure Click here
A0A1D6LA85 View 3D Structure Click here
A0A1D6LA85 View 3D Structure Click here
A0A1D6LGF9 View 3D Structure Click here
A0A1D6MDK0 View 3D Structure Click here
A0A1D6MXH1 View 3D Structure Click here
A0A1D6N382 View 3D Structure Click here
A0A1D6N382 View 3D Structure Click here
A0A1D6N382 View 3D Structure Click here
A0A1D6N382 View 3D Structure Click here
A0A1D6N382 View 3D Structure Click here
A0A1D6NA34 View 3D Structure Click here
A0A1D6NHL1 View 3D Structure Click here
A0A1D6NMC0 View 3D Structure Click here
A0A1D6NMC0 View 3D Structure Click here
A0A1D6NMC0 View 3D Structure Click here
A0A1D6PB88 View 3D Structure Click here
A0A1D6PZH9 View 3D Structure Click here
A0A1D8PJ76 View 3D Structure Click here
A0A1D8PKD4 View 3D Structure Click here
A0A1D8PSG9 View 3D Structure Click here
A0A1D8PSG9 View 3D Structure Click here
A0A1P8AM37 View 3D Structure Click here
A0A2K5ATS7 View 3D Structure Click here
A0A2R8PZG8 View 3D Structure Click here
A0A2R8RWQ9 View 3D Structure Click here
A2ZVY5 View 3D Structure Click here
A3BUD2 View 3D Structure Click here
A3KPX4 View 3D Structure Click here
A4HRT0 View 3D Structure Click here
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A4HSS9 View 3D Structure Click here
A4HWB1 View 3D Structure Click here
A4HZP4 View 3D Structure Click here
A4I363 View 3D Structure Click here
A4I3B4 View 3D Structure Click here
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A4I5V6 View 3D Structure Click here
A4I648 View 3D Structure Click here
A4I7Y9 View 3D Structure Click here
A4IAZ9 View 3D Structure Click here
A4IB01 View 3D Structure Click here
A4IB52 View 3D Structure Click here
A4IC38 View 3D Structure Click here
A9UH06 View 3D Structure Click here
A9UH12 View 3D Structure Click here
A9UH12 View 3D Structure Click here
B4FAF4 View 3D Structure Click here
B4FAF4 View 3D Structure Click here
B4FAP0 View 3D Structure Click here
B4FAP0 View 3D Structure Click here
B4FAP0 View 3D Structure Click here
B4FAP0 View 3D Structure Click here
B4FAP0 View 3D Structure Click here
B4FAX8 View 3D Structure Click here
B4FAX8 View 3D Structure Click here
B4FB09 View 3D Structure Click here
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B4FCG2 View 3D Structure Click here
B4FE66 View 3D Structure Click here
B4FE66 View 3D Structure Click here
B4FQ72 View 3D Structure Click here
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B4FTY3 View 3D Structure Click here
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B4FTY3 View 3D Structure Click here
B4FWN6 View 3D Structure Click here
B6SW16 View 3D Structure Click here
B6T886 View 3D Structure Click here
B6TRJ7 View 3D Structure Click here
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B6TV15 View 3D Structure Click here
B6TV15 View 3D Structure Click here
B6TV15 View 3D Structure Click here
B6TV15 View 3D Structure Click here
B6TV15 View 3D Structure Click here
B6U194 View 3D Structure Click here
B7ZYH4 View 3D Structure Click here
B8JIV1 View 3D Structure Click here
B8JIV1 View 3D Structure Click here
C0H566 View 3D Structure Click here
C0P5G8 View 3D Structure Click here
C0P5G8 View 3D Structure Click here
C0P642 View 3D Structure Click here
C0P642 View 3D Structure Click here
C0P642 View 3D Structure Click here
C0P642 View 3D Structure Click here
C0P642 View 3D Structure Click here
C0PFP1 View 3D Structure Click here
C6TA41 View 3D Structure Click here
C6TA41 View 3D Structure Click here
D3ZBM2 View 3D Structure Click here
D3ZHK9 View 3D Structure Click here
D3ZHK9 View 3D Structure Click here
D3ZHQ8 View 3D Structure Click here
D3ZKY5 View 3D Structure Click here
D3ZLD2 View 3D Structure Click here
D3ZLM7 View 3D Structure Click here
D3ZV40 View 3D Structure Click here
D3ZVW3 View 3D Structure Click here
D4A3S7 View 3D Structure Click here
D4A3V3 View 3D Structure Click here
D4AA59 View 3D Structure Click here
D4ADZ6 View 3D Structure Click here
E7EXP6 View 3D Structure Click here
E7F2A1 View 3D Structure Click here
E7F3S4 View 3D Structure Click here
E7F3S4 View 3D Structure Click here
E7FC88 View 3D Structure Click here
E7FH07 View 3D Structure Click here
E9PSN4 View 3D Structure Click here
E9Q784 View 3D Structure Click here
F1LTU5 View 3D Structure Click here
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F1M1R4 View 3D Structure Click here
F1Q4N1 View 3D Structure Click here
F1Q639 View 3D Structure Click here
F1Q949 View 3D Structure Click here
F1QGD9 View 3D Structure Click here
F1QH59 View 3D Structure Click here
F1QH59 View 3D Structure Click here
F1QU82 View 3D Structure Click here
F1QU82 View 3D Structure Click here
F1RB94 View 3D Structure Click here
F1RB94 View 3D Structure Click here
F1RCP3 View 3D Structure Click here
F1RCP3 View 3D Structure Click here
F1RCT4 View 3D Structure Click here
F2Z3T4 View 3D Structure Click here
F2Z3T4 View 3D Structure Click here
F8VPP8 View 3D Structure Click here
F8VPP8 View 3D Structure Click here
F8W2E8 View 3D Structure Click here
G5EC86 View 3D Structure Click here
G5EC86 View 3D Structure Click here
G5ECB9 View 3D Structure Click here
G5ECB9 View 3D Structure Click here
G5EF15 View 3D Structure Click here
G5EF15 View 3D Structure Click here
I1J4E8 View 3D Structure Click here
I1J6A5 View 3D Structure Click here
I1J6A5 View 3D Structure Click here
I1JAF9 View 3D Structure Click here
I1JFH0 View 3D Structure Click here
I1JFH0 View 3D Structure Click here
I1JFH0 View 3D Structure Click here
I1JFH0 View 3D Structure Click here
I1JFH1 View 3D Structure Click here
I1JFH1 View 3D Structure Click here
I1JFH1 View 3D Structure Click here
I1JFH1 View 3D Structure Click here
I1JFH1 View 3D Structure Click here
I1JG21 View 3D Structure Click here
I1JG21 View 3D Structure Click here
I1JHC2 View 3D Structure Click here
I1JHD2 View 3D Structure Click here
I1JJF9 View 3D Structure Click here
I1JKM9 View 3D Structure Click here
I1JNK1 View 3D Structure Click here
I1JNK1 View 3D Structure Click here
I1JNK3 View 3D Structure Click here
I1JNK3 View 3D Structure Click here
I1JPW6 View 3D Structure Click here
I1JPW6 View 3D Structure Click here
I1JTV7 View 3D Structure Click here
I1JXF6 View 3D Structure Click here
I1JXF6 View 3D Structure Click here
I1JXF6 View 3D Structure Click here
I1JXF6 View 3D Structure Click here
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I1K073 View 3D Structure Click here
I1K073 View 3D Structure Click here
I1K073 View 3D Structure Click here
I1K073 View 3D Structure Click here
I1K073 View 3D Structure Click here
I1K1F1 View 3D Structure Click here
I1K1F1 View 3D Structure Click here
I1K618 View 3D Structure Click here
I1K8B1 View 3D Structure Click here
I1KBI1 View 3D Structure Click here
I1KEZ7 View 3D Structure Click here
I1KJS9 View 3D Structure Click here
I1KKN4 View 3D Structure Click here
I1KKN4 View 3D Structure Click here
I1KN18 View 3D Structure Click here
I1KN18 View 3D Structure Click here
I1KN18 View 3D Structure Click here
I1KN18 View 3D Structure Click here
I1KN18 View 3D Structure Click here
I1KPU6 View 3D Structure Click here
I1KTL8 View 3D Structure Click here
I1KW27 View 3D Structure Click here
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I1KW27 View 3D Structure Click here
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I1KW27 View 3D Structure Click here
I1KXE8 View 3D Structure Click here
I1L2G5 View 3D Structure Click here
I1L6B1 View 3D Structure Click here
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I1L6B1 View 3D Structure Click here
I1L6B1 View 3D Structure Click here
I1L7X3 View 3D Structure Click here
I1L7X3 View 3D Structure Click here
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I1LAB5 View 3D Structure Click here
I1LB10 View 3D Structure Click here
I1LBV8 View 3D Structure Click here
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I1LBV8 View 3D Structure Click here
I1LBV8 View 3D Structure Click here
I1LFK3 View 3D Structure Click here
I1LFK3 View 3D Structure Click here
I1LG60 View 3D Structure Click here
I1LJ34 View 3D Structure Click here
I1LNZ5 View 3D Structure Click here
I1LS62 View 3D Structure Click here
I1LTR2 View 3D Structure Click here
I1LTR2 View 3D Structure Click here
I1LUH8 View 3D Structure Click here
I1LVD6 View 3D Structure Click here
I1M0Y0 View 3D Structure Click here
I1M1E0 View 3D Structure Click here
I1M1E0 View 3D Structure Click here
I1M1E0 View 3D Structure Click here
I1M1E0 View 3D Structure Click here
I1M6I7 View 3D Structure Click here
I1M6J5 View 3D Structure Click here
I1MBA2 View 3D Structure Click here
I1MBB4 View 3D Structure Click here
I1MF45 View 3D Structure Click here
I1MF45 View 3D Structure Click here
I1MF45 View 3D Structure Click here
I1MF45 View 3D Structure Click here
I1MJM7 View 3D Structure Click here
I1MJP7 View 3D Structure Click here
I1MUL4 View 3D Structure Click here
I1MUL4 View 3D Structure Click here
I1MUL4 View 3D Structure Click here
I1MUL4 View 3D Structure Click here
I1MUL4 View 3D Structure Click here
I1N3Y4 View 3D Structure Click here
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I1N3Y4 View 3D Structure Click here
I1N3Y4 View 3D Structure Click here
I1N3Y4 View 3D Structure Click here
I1N979 View 3D Structure Click here
I1N979 View 3D Structure Click here
I1NAI8 View 3D Structure Click here
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I1ND08 View 3D Structure Click here
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I1NIJ3 View 3D Structure Click here
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I1NIJ3 View 3D Structure Click here
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I1NIJ3 View 3D Structure Click here
K7KAZ9 View 3D Structure Click here
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K7KR55 View 3D Structure Click here
K7KS04 View 3D Structure Click here
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K7LTE4 View 3D Structure Click here
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K7M3X6 View 3D Structure Click here
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K7MA73 View 3D Structure Click here
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K7ML60 View 3D Structure Click here
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K7N2I8 View 3D Structure Click here
K7UB91 View 3D Structure Click here
K7UB91 View 3D Structure Click here
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K7V1E2 View 3D Structure Click here
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K7VP35 View 3D Structure Click here
M0RBK3 View 3D Structure Click here
M0RBK3 View 3D Structure Click here
O02289 View 3D Structure Click here
O02289 View 3D Structure Click here
O15541 View 3D Structure Click here
O17917 View 3D Structure Click here
O18251 View 3D Structure Click here
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O45289 View 3D Structure Click here
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O48772 View 3D Structure Click here
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O55000 View 3D Structure Click here
O65036 View 3D Structure Click here
O74463 View 3D Structure Click here
O74823 View 3D Structure Click here
O95639 View 3D Structure Click here
P0C090 View 3D Structure Click here
P0DN76 View 3D Structure Click here
P0DN76 View 3D Structure Click here
P17431 View 3D Structure Click here
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P22893 View 3D Structure Click here
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