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38  structures 1406  species 0  interactions 19061  sequences 579  architectures

Family: zf-CCCH_2 (PF14608)

Summary: RNA-binding, Nab2-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.

RNA-binding, Nab2-type zinc finger Provide feedback

This is an unusual zinc-finger family, and is represented by fingers 5-7 of Nab2. Nab2 ZnF5-7 are zinc-fingers of the type C-x8-C-x5-C-x3-H. Nab2 ZnFs function in the generation of export-competent mRNPs. Mab2 is a conserved polyadenosine-RNA-binding Zn finger protein required for both mRNA export and polyadenylation regulation and becomes attached to the mRNP after splicing and during or immediately after polyadenylation. The three ZnFs, 5-7, have almost identical folds and, most unusually, associate with one another to form a single coherent structural unit. ZnF5-7 bind to eight consecutive adenines, and chemical shift perturbations identify residues on each finger that interact with RNA [1].

Literature references

  1. Brockmann C, Soucek S, Kuhlmann SI, Mills-Lujan K, Kelly SM, Yang JC, Iglesias N, Stutz F, Corbett AH, Neuhaus D, Stewart M;, Structure. 2012;20:1007-1018.: Structural basis for polyadenosine-RNA binding by Nab2 Zn fingers and its function in mRNA nuclear export. PUBMED:22560733 EPMC:22560733


Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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
(156)
Full
(19061)
Representative proteomes UniProt
(32591)
RP15
(2254)
RP35
(6799)
RP55
(15038)
RP75
(21629)
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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

  Seed
(156)
Full
(19061)
Representative proteomes UniProt
(32591)
RP15
(2254)
RP35
(6799)
RP55
(15038)
RP75
(21629)
Alignment:
Format:
Order:
Sequence:
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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
(156)
Full
(19061)
Representative proteomes UniProt
(32591)
RP15
(2254)
RP35
(6799)
RP55
(15038)
RP75
(21629)
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: Pfam-B_880 (release 26.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Wood V , Coggill P
Number in seed: 156
Number in full: 19061
Average length of the domain: 19.40 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 8.26 %

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 25.8 8.0
Trusted cut-off 25.8 8.0
Noise cut-off 25.7 7.9
Model length: 19
Family (HMM) version: 8
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_2 domain has been found. There are 38 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
A0A096Q3U9 View 3D Structure Click here
A0A096Q3U9 View 3D Structure Click here
A0A0G2JX72 View 3D Structure Click here
A0A0G2JX72 View 3D Structure Click here
A0A0G2JX72 View 3D Structure Click here
A0A0G2QC40 View 3D Structure Click here
A0A1D6FZC1 View 3D Structure Click here
A0A1D6IUH6 View 3D Structure Click here
A0A1D6IUH6 View 3D Structure Click here
A0A1D6J754 View 3D Structure Click here
A0A1D6J754 View 3D Structure Click here
A0A1D6J754 View 3D Structure Click here
A0A1D6J754 View 3D Structure Click here
A0A1D6L005 View 3D Structure Click here
A0A1D6NMC0 View 3D Structure Click here
A0A1D6NZP1 View 3D Structure Click here
A0A1D6NZP1 View 3D Structure Click here
A0A1D6NZP1 View 3D Structure Click here
A0A1D8PCH2 View 3D Structure Click here
A0A1D8PCH2 View 3D Structure Click here
A0A1D8PCH2 View 3D Structure Click here
A0A1D8PCH2 View 3D Structure Click here
A0A1D8PKD4 View 3D Structure Click here
A0A2R8RJV4 View 3D Structure Click here
A0A2R8RJV4 View 3D Structure Click here
A0A2R8RVJ0 View 3D Structure Click here
A0A2R8RVJ0 View 3D Structure Click here
A4HTZ3 View 3D Structure Click here
A4HTZ3 View 3D Structure Click here
A4HTZ3 View 3D Structure Click here
A6NMK7 View 3D Structure Click here
A6NMK7 View 3D Structure Click here
A9UH06 View 3D Structure Click here
A9UH06 View 3D Structure Click here
A9UH06 View 3D Structure Click here
A9UH12 View 3D Structure Click here
A9UH12 View 3D Structure Click here
B4FB09 View 3D Structure Click here
B8JIV1 View 3D Structure Click here
B8JIV1 View 3D Structure Click here
C6KT67 View 3D Structure Click here
C6KT67 View 3D Structure Click here
C6KT67 View 3D Structure Click here
C6TA41 View 3D Structure Click here
D3ZLM7 View 3D Structure Click here
D3ZLM7 View 3D Structure Click here
D3ZQV3 View 3D Structure Click here
D3ZQV3 View 3D Structure Click here
D3ZQV3 View 3D Structure Click here
D3ZVW3 View 3D Structure Click here
D3ZY41 View 3D Structure Click here
D3ZY41 View 3D Structure Click here
E0X9N4 View 3D Structure Click here
E0X9N4 View 3D Structure Click here
E7FGZ9 View 3D Structure Click here
E7FGZ9 View 3D Structure Click here
F1LTU5 View 3D Structure Click here
F1Q6H4 View 3D Structure Click here
F1Q6H4 View 3D Structure Click here
F2Z3T4 View 3D Structure Click here
F2Z3T4 View 3D Structure Click here
I1JG21 View 3D Structure Click here
I1JNK1 View 3D Structure Click here
I1JNK3 View 3D Structure Click here
I1K3A1 View 3D Structure Click here
I1KBI1 View 3D Structure Click here
I1KRM9 View 3D Structure Click here
I1KTL8 View 3D Structure Click here
I1KTL8 View 3D Structure Click here
I1LFK3 View 3D Structure Click here
I1MJM5 View 3D Structure Click here
I1MJM5 View 3D Structure Click here
I1MJM7 View 3D Structure Click here
I1MJM7 View 3D Structure Click here
I1N979 View 3D Structure Click here
K7KLH6 View 3D Structure Click here
K7TI82 View 3D Structure Click here
K7UZL9 View 3D Structure Click here
P32505 View 3D Structure Click here
P32505 View 3D Structure Click here
P32505 View 3D Structure Click here
P32505 View 3D Structure Click here
P41000 View 3D Structure Click here
P61129 View 3D Structure Click here
Q0J952 View 3D Structure Click here
Q13064 View 3D Structure Click here
Q13064 View 3D Structure Click here
Q13434 View 3D Structure Click here
Q2QTY2 View 3D Structure Click here
Q3TIV5 View 3D Structure Click here
Q4VBT5 View 3D Structure Click here
Q55BM8 View 3D Structure Click here
Q55BM8 View 3D Structure Click here
Q55BM8 View 3D Structure Click here
Q55BM8 View 3D Structure Click here
Q55BM8 View 3D Structure Click here
Q55BM8 View 3D Structure Click here
Q55CA3 View 3D Structure Click here
Q59T36 View 3D Structure Click here
Q59T36 View 3D Structure Click here
Q59T36 View 3D Structure Click here
Q5TYQ8 View 3D Structure Click here
Q5TYQ8 View 3D Structure Click here
Q5TYQ8 View 3D Structure Click here
Q5TYQ8 View 3D Structure Click here
Q5TYQ8 View 3D Structure Click here
Q5VZF2 View 3D Structure Click here
Q5VZF2 View 3D Structure Click here
Q5XI23 View 3D Structure Click here
Q5ZA07 View 3D Structure Click here
Q5ZA07 View 3D Structure Click here
Q60764 View 3D Structure Click here
Q60764 View 3D Structure Click here
Q6AT25 View 3D Structure Click here
Q6AYB0 View 3D Structure Click here
Q6IDS6 View 3D Structure Click here
Q6K977 View 3D Structure Click here
Q6PJT7 View 3D Structure Click here
Q6PJT7 View 3D Structure Click here
Q6PJT7 View 3D Structure Click here
Q6PJT7 View 3D Structure Click here
Q6PJT7 View 3D Structure Click here
Q6U6G5 View 3D Structure Click here
Q6YYC0 View 3D Structure Click here
Q6YYC0 View 3D Structure Click here
Q6ZPZ3 View 3D Structure Click here
Q7F8R0 View 3D Structure Click here
Q7TMD5 View 3D Structure Click here
Q7TMD5 View 3D Structure Click here
Q7TMD5 View 3D Structure Click here
Q7TMD5 View 3D Structure Click here
Q7TMD5 View 3D Structure Click here
Q7XPK1 View 3D Structure Click here
Q803J8 View 3D Structure Click here
Q8BJ05 View 3D Structure Click here
Q8BJ05 View 3D Structure Click here
Q8BJ05 View 3D Structure Click here
Q8BJ05 View 3D Structure Click here
Q8BJ05 View 3D Structure Click here
Q8BYK8 View 3D Structure Click here
Q8C181 View 3D Structure Click here
Q8C181 View 3D Structure Click here
Q8IJV8 View 3D Structure Click here
Q8IJV8 View 3D Structure Click here
Q8N5P1 View 3D Structure Click here
Q8R003 View 3D Structure Click here
Q8R003 View 3D Structure Click here
Q8R003 View 3D Structure Click here
Q8R205 View 3D Structure Click here
Q8R205 View 3D Structure Click here
Q95XU6 View 3D Structure Click here
Q95XU6 View 3D Structure Click here
Q95XU6 View 3D Structure Click here
Q95XU6 View 3D Structure Click here
Q96K80 View 3D Structure Click here
Q96K80 View 3D Structure Click here
Q9C7C3 View 3D Structure Click here
Q9DFG8 View 3D Structure Click here
Q9ERV1 View 3D Structure Click here
Q9H000 View 3D Structure Click here
Q9JJ48 View 3D Structure Click here
Q9JKP5 View 3D Structure Click here
Q9JKP5 View 3D Structure Click here
Q9JKP5 View 3D Structure Click here
Q9LT81 View 3D Structure Click here
Q9N373 View 3D Structure Click here
Q9N373 View 3D Structure Click here
Q9NR56 View 3D Structure Click here
Q9NR56 View 3D Structure Click here
Q9NR56 View 3D Structure Click here
Q9NUK0 View 3D Structure Click here
Q9NUK0 View 3D Structure Click here
Q9NUK0 View 3D Structure Click here
Q9QXP6 View 3D Structure Click here
Q9UHC7 View 3D Structure Click here
Q9UPT8 View 3D Structure Click here
Q9V3H9 View 3D Structure Click here
Q9V3H9 View 3D Structure Click here
Q9V3H9 View 3D Structure Click here
Q9VP20 View 3D Structure Click here
Q9VY20 View 3D Structure Click here
Q9ZUM0 View 3D Structure Click here