Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
22  structures 1543  species 0  interactions 4380  sequences 103  architectures

Family: OB_Dis3 (PF17849)

Summary: Dis3-like cold-shock domain 2 (CSD2)

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

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.

Dis3-like cold-shock domain 2 (CSD2) Provide feedback

This domain has an OB fold and is found in the Dis3l2 protein [1]. This domain along with CSD1 binds to RNA.

Literature references

  1. Faehnle CR, Walleshauser J, Joshua-Tor L;, Nature. 2014;514:252-256.: Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway. PUBMED:25119025 EPMC:25119025

  2. Lorentzen E, Basquin J, Tomecki R, Dziembowski A, Conti E;, Mol Cell. 2008;29:717-728.: Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. PUBMED:18374646 EPMC:18374646

  3. Bonneau F, Basquin J, Ebert J, Lorentzen E, Conti E;, Cell. 2009;139:547-559.: The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. PUBMED:19879841 EPMC:19879841

  4. Makino DL, Baumgartner M, Conti E;, Nature. 2013;495:70-75.: Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. PUBMED:23376952 EPMC:23376952


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR041505

This domain has an OB fold and is found in the Dis3l2 protein [ PUBMED:25119025 ]. This domain along with CSD1 binds to RNA.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

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
(75)
Full
(4380)
Representative proteomes UniProt
(7067)
RP15
(830)
RP35
(1874)
RP55
(3330)
RP75
(4472)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(75)
Full
(4380)
Representative proteomes UniProt
(7067)
RP15
(830)
RP35
(1874)
RP55
(3330)
RP75
(4472)
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
(75)
Full
(4380)
Representative proteomes UniProt
(7067)
RP15
(830)
RP35
(1874)
RP55
(3330)
RP75
(4472)
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: ECOD:EUF00584
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 75
Number in full: 4380
Average length of the domain: 72.20 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 7.04 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.8 22.8
Trusted cut-off 22.8 22.8
Noise cut-off 22.7 22.7
Model length: 77
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 OB_Dis3 domain has been found. There are 22 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.

Loading structure mapping...

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
A0A0G2K6W6 View 3D Structure Click here
A0A0N7KGI5 View 3D Structure Click here
A0A0R0GK53 View 3D Structure Click here
A2RV18 View 3D Structure Click here
A4I3B7 View 3D Structure Click here
C0H520 View 3D Structure Click here
C0HGV6 View 3D Structure Click here
E7F350 View 3D Structure Click here
E7FE01 View 3D Structure Click here
F7EPZ4 View 3D Structure Click here
I1JYB3 View 3D Structure Click here
I1KB85 View 3D Structure Click here
I1LUV0 View 3D Structure Click here
I1MAK8 View 3D Structure Click here
K7UA17 View 3D Structure Click here
O14040 View 3D Structure Click here
O74454 View 3D Structure Click here
O94525 View 3D Structure Click here
P24276 View 3D Structure Click here
P37202 View 3D Structure Click here
Q08162 View 3D Structure Click here
Q09568 View 3D Structure Click here
Q0WPN0 View 3D Structure Click here
Q17632 View 3D Structure Click here
Q4DG23 View 3D Structure Click here
Q54BH9 View 3D Structure Click here
Q54XT5 View 3D Structure Click here
Q55FB1 View 3D Structure Click here
Q5A3P1 View 3D Structure Click here
Q5AK62 View 3D Structure Click here
Q5U2P0 View 3D Structure Click here
Q6Z6A3 View 3D Structure Click here
Q8C0S1 View 3D Structure Click here
Q8CI75 View 3D Structure Click here
Q8IDB6 View 3D Structure Click here
Q8IRJ7 View 3D Structure Click here
Q8IYB7 View 3D Structure Click here
Q8TF46 View 3D Structure Click here
Q9CSH3 View 3D Structure Click here
Q9SHL7 View 3D Structure Click here