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0  structures 228  species 0  interactions 282  sequences 8  architectures

Family: PMC2NT (PF08066)

Summary: PMC2NT (NUC016) domain

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PMC2NT (NUC016) domain Provide feedback

This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components [1].

Literature references

  1. Staub E, Fiziev P, Rosenthal A, Hinzmann B; , Bioessays 2004;26:567-581.: Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire. PUBMED:15112237 EPMC:15112237


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012588

Exosomes are nano-compartments that function in the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA) [PUBMED:15951817, PUBMED:17174896]. Exosomes occur in both archaea and eukaryotes, and have a similar overall structure to each other and to bacterial/organelle PNPases (polynucleotide phosphorylases; EC) [PUBMED:17084501], consisting of a barrel structure composed of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber [PUBMED:16285927]. There are two types of exosomes in eukaryotes, cytoplasmic exosomes that are responsible for 3'-5' exoribonuclease degradation of mRNAs, and nuclear exosomes that degrade pre-mRNAs (such as nonsense transcripts) and degrade rRNAs, snRNAs and snoRNAs. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [PUBMED:16713559, PUBMED:17380186].

There are several accessory proteins that help degrade, unwind or polyadenylate RNA substrate before they enter the exosome. This entry represents the N-terminal domain of Rrp6 (exosome component 10 in humans), a nuclear exosome accessory factor that interacts with the bottom of the hexameric PH-ring opposite the cap. Rrp6 functions as a hydrolytic exonuclease, and is homologous to RNase-D in Escherichia coli.

More information about these proteins can be found at Protein of the Month: RNA Exosomes [PUBMED:].

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(31)
Full
(282)
Representative proteomes NCBI
(278)
Meta
(0)
RP15
(54)
RP35
(90)
RP55
(143)
RP75
(176)
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Pfam viewer View  View             

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

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

Format an alignment

  Seed
(31)
Full
(282)
Representative proteomes NCBI
(278)
Meta
(0)
RP15
(54)
RP35
(90)
RP55
(143)
RP75
(176)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(31)
Full
(282)
Representative proteomes NCBI
(278)
Meta
(0)
RP15
(54)
RP35
(90)
RP55
(143)
RP75
(176)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Staub E
Previous IDs: none
Type: Domain
Author: Staub E, Bateman A
Number in seed: 31
Number in full: 282
Average length of the domain: 91.50 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 11.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.2 22.2
Trusted cut-off 22.5 22.5
Noise cut-off 22.0 21.8
Model length: 91
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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