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7  structures 308  species 0  interactions 4588  sequences 77  architectures

Family: zf-C2HC (PF01530)

Summary: Zinc finger, C2HC type

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

This is the Wikipedia entry entitled "Zinc finger". More...

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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.

Zinc finger, C2HC type Provide feedback

This is a DNA binding zinc finger domain.

Literature references

  1. Kim JG, Hudson LD; , Mol Cell Biol 1992;12:5632-5639.: Novel member of the zinc finger superfamily: A C2-HC finger that recognizes a glia-specific gene. PUBMED:1280325 EPMC:1280325


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002515

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 the CysCysHisHisCys (CCHHC) type zinc finger domain found in eukaryotes. The CCHHC-type zinc finger contains five absolutely conserved cysteine and histidine residues (rather than the more usual four) with the sequence C-P-x-P-G-C-x-G-x-G-H-x(7)-H-R-x(4)-C. The second histidine has been shown to coordinate Zn(II) along with the three cysteines residues. The first His plays a different role in stabilizing the structure, stacking between the metal-binding core and an aromatic residue that is relatively conserved. CCHHC-type zinc fingers form small compact structures that can sit entirely within the major groove of DNA [PUBMED:18073212, PUBMED:24097990, PUBMED:25098749, PUBMED:26158299, PUBMED:14744132].

Some proteins known to contain a CCHHC-type zinc finger are listed below:

  • Animal myelin transcription factor 1 (MyT1), or neural zinc finger 2 (NZF2), a transcription factor that contains seven copies of the CCHHC-type zinc finger. It binds to sites in the proteolipid protein promoter.
  • Vertebrate MyT1-like (MyT1L/NZF1), appears to be involved in neural development.
  • Vertebrate Suppressor of Tumorigenicity 18 (ST18/NZF3), a breast cancer tumour suppressor.
  • Vertebrate L3MBTL, a member of the Polycomb group of proteins, which function as transcriptional repressors in large protein complexes.
  • Vertebrate L3MBTL3, a possible tumor suppressor.
  • Vertebrate L3MBTL4.

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, the UniProtKB sequence database, 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
(82)
Full
(4588)
Representative proteomes UniProt
(6646)
NCBI
(22352)
Meta
(1)
RP15
(603)
RP35
(1457)
RP55
(2809)
RP75
(3431)
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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
(82)
Full
(4588)
Representative proteomes UniProt
(6646)
NCBI
(22352)
Meta
(1)
RP15
(603)
RP35
(1457)
RP55
(2809)
RP75
(3431)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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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
(82)
Full
(4588)
Representative proteomes UniProt
(6646)
NCBI
(22352)
Meta
(1)
RP15
(603)
RP35
(1457)
RP55
(2809)
RP75
(3431)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Swiss-Prot
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 82
Number in full: 4588
Average length of the domain: 28.70 aa
Average identity of full alignment: 65 %
Average coverage of the sequence by the domain: 10.36 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.7
Model length: 29
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Selections

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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-C2HC domain has been found. There are 7 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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