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37  structures 1167  species 0  interactions 6896  sequences 192  architectures

Family: ArgoL2 (PF16488)

Summary: Argonaute linker 2 domain

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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.

Argonaute linker 2 domain Provide feedback

ArgoL2 is the second linker domain in eukaryotic argonaute proteins. It starts with two alpha-helices aligned orthogonally to each other followed by a beta-strand involved in linking the two lobes, the PAZ lobe and the Piwi lobe of argonaute to each other. Linker 2 together with the N, PAZ and L1 domains form a compact global fold [1]. Numerous residues from Piwi, L1 and L2 linkers direct the path of the phosphate backbone of nucleotides 7-9, thus allowing DNA-slicing [2].

Literature references

  1. Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T, Patel DJ;, Mol Cell. 2005;19:405-419.: Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. PUBMED:16061186 EPMC:16061186

  2. Faehnle CR, Elkayam E, Haase AD, Hannon GJ, Joshua-Tor L;, Cell Rep. 2013;3:1901-1909.: The making of a slicer: activation of human Argonaute-1. PUBMED:23746446 EPMC:23746446


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR032472

ArgoL2 is the second linker domain in eukaryotic argonaute proteins. It starts with two alpha-helices aligned orthogonally to each other followed by a beta-strand involved in linking the two lobes, the PAZ lobe and the Piwi lobe of argonaute to each other. Linker 2 together with the N, PAZ and L1 domains form a compact global fold [ PUBMED:16061186 ]. Numerous residues from Piwi, L1 and L2 linkers direct the path of the phosphate backbone of nucleotides 7-9, thus allowing DNA-slicing [ PUBMED:23746446 ].

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 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
(337)
Full
(6896)
Representative proteomes UniProt
(10534)
RP15
(729)
RP35
(2772)
RP55
(5377)
RP75
(7381)
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
(337)
Full
(6896)
Representative proteomes UniProt
(10534)
RP15
(729)
RP35
(2772)
RP55
(5377)
RP75
(7381)
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
(337)
Full
(6896)
Representative proteomes UniProt
(10534)
RP15
(729)
RP35
(2772)
RP55
(5377)
RP75
(7381)
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: [1]
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P , Bateman A
Number in seed: 337
Number in full: 6896
Average length of the domain: 47.30 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 5.34 %

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 33.3 33.3
Trusted cut-off 33.3 33.3
Noise cut-off 33.2 33.2
Model length: 47
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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 ArgoL2 domain has been found. There are 37 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
A0A0P0V142 View 3D Structure Click here
A0A0P0W4J5 View 3D Structure Click here
A0A0R0I9G1 View 3D Structure Click here
A0A1D6DZF2 View 3D Structure Click here
A0A1D6E2V1 View 3D Structure Click here
A0A1D6EVH9 View 3D Structure Click here
A0A1D6F8V7 View 3D Structure Click here
A0A1D6FB88 View 3D Structure Click here
A0A1D6FWE3 View 3D Structure Click here
A0A1D6GFG2 View 3D Structure Click here
A0A1D6GKG3 View 3D Structure Click here
A0A1D6GWY2 View 3D Structure Click here
A0A1D6I0T3 View 3D Structure Click here
A0A1D6IAA8 View 3D Structure Click here
A0A1D6JCD6 View 3D Structure Click here
A0A1D6KZF1 View 3D Structure Click here
A0A1D6LIA5 View 3D Structure Click here
A0A1D6LSG3 View 3D Structure Click here
A0A1D6MEK7 View 3D Structure Click here
A0A1D6MQQ3 View 3D Structure Click here
A0A1D6P2M1 View 3D Structure Click here
A3KPK0 View 3D Structure Click here
D4AC38 View 3D Structure Click here
E7EXY4 View 3D Structure Click here
F1LUQ5 View 3D Structure Click here
F1LUS2 View 3D Structure Click here
F1Q7S8 View 3D Structure Click here
G5ED77 View 3D Structure Click here
G5EES3 View 3D Structure Click here
I1JB56 View 3D Structure Click here
I1JIR2 View 3D Structure Click here
I1LDY9 View 3D Structure Click here
I1LRB1 View 3D Structure Click here
I1M7A2 View 3D Structure Click here
I1MQL3 View 3D Structure Click here
I1MUE1 View 3D Structure Click here
I1NGL2 View 3D Structure Click here
K4IAH1 View 3D Structure Click here
K7KK31 View 3D Structure Click here
K7KNI8 View 3D Structure Click here
K7KWE6 View 3D Structure Click here
K7LQ94 View 3D Structure Click here
K7MB18 View 3D Structure Click here
K7N1Q0 View 3D Structure Click here
O04379 View 3D Structure Click here
O16720 View 3D Structure Click here
O48771 View 3D Structure Click here
O74957 View 3D Structure Click here
P34681 View 3D Structure Click here
Q0JF58 View 3D Structure Click here
Q10F39 View 3D Structure Click here
Q32KD4 View 3D Structure Click here
Q3E984 View 3D Structure Click here
Q5NBN9 View 3D Structure Click here
Q5Z5B2 View 3D Structure Click here
Q69UP6 View 3D Structure Click here
Q69VD5 View 3D Structure Click here
Q6EU14 View 3D Structure Click here
Q6H6C3 View 3D Structure Click here
Q6K972 View 3D Structure Click here
Q6YSJ5 View 3D Structure Click here
Q6Z4F1 View 3D Structure Click here
Q7XSA2 View 3D Structure Click here
Q7XTS4 View 3D Structure Click here
Q7Y001 View 3D Structure Click here
Q84VQ0 View 3D Structure Click here
Q851R2 View 3D Structure Click here
Q852N2 View 3D Structure Click here
Q8CJF8 View 3D Structure Click here
Q8CJF9 View 3D Structure Click here
Q8CJG0 View 3D Structure Click here
Q8CJG1 View 3D Structure Click here
Q9H9G7 View 3D Structure Click here
Q9HCK5 View 3D Structure Click here
Q9QZ81 View 3D Structure Click here
Q9SDG8 View 3D Structure Click here
Q9SHF2 View 3D Structure Click here
Q9SHF3 View 3D Structure Click here
Q9SJK3 View 3D Structure Click here
Q9UKV8 View 3D Structure Click here
Q9UL18 View 3D Structure Click here
Q9VUQ5 View 3D Structure Click here
Q9XGW1 View 3D Structure Click here
Q9XVI3 View 3D Structure Click here
Q9ZVD5 View 3D Structure Click here
X1WG39 View 3D Structure Click here