Summary: RNA-binding, Nab2-type zinc finger
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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
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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
SCOOP: | RWD Torus zf-CCCH zf-CCCH_3 zf-CCCH_4 zf_CCCH_4 |
Similarity to PfamA using HHSearch: | zf-CCCH zf-CCCH_3 zf-CCCH_4 zf_CCCH_4 |
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_5Alignments
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.
Seed (156) |
Full (23330) |
Representative proteomes | UniProt (35606) |
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RP15 (2694) |
RP35 (7462) |
RP55 (16599) |
RP75 (23653) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (156) |
Full (23330) |
Representative proteomes | UniProt (35606) |
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---|---|---|---|---|---|---|---|
RP15 (2694) |
RP35 (7462) |
RP55 (16599) |
RP75 (23653) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Pfam-B_880 (release 26.0) |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Wood V |
Number in seed: | 156 |
Number in full: | 23330 |
Average length of the domain: | 19.4 aa |
Average identity of full alignment: | 39 % |
Average coverage of the sequence by the domain: | 8.33 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 19 | ||||||||||||
Family (HMM) version: | 9 | ||||||||||||
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.