!!

Powering down the Pfam website
On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

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.
58  structures 4064  species 0  interactions 7775  sequences 118  architectures

Family: Ku (PF02735)

Summary: Ku70/Ku80 beta-barrel domain

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

This is the Wikipedia entry entitled "Ku (protein)". More...

Ku (protein) Edit Wikipedia article

The Ku protein is a heterodimer of polypeptides of around 70kDa and 80 kDa. Its function is to bind to DNA double-strand breaks.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Ku70/Ku80 beta-barrel domain Provide feedback

The Ku heterodimer (composed of Ku70 P12956 and Ku80 P13010) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 P12956 and Ku80 P13010 proteins that form a DNA binding heterodimer [1].

Literature references

  1. Walker JR, Corpina RA, Goldberg J; , Nature 2001;412:607-614.: Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair. PUBMED:11493912 EPMC:11493912

  2. Aravind L, Koonin EV; , Genome Res 2001;11:1365-1374.: Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. PUBMED:11483577 EPMC:11483577


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006164

The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 and Ku80 proteins that form a DNA binding heterodimer [ PUBMED:11493912 ].

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan SPOC (CL0616), which has the following description:

The crystal structure of the SPOC domain [3] showed it has similarity with the beta barrel domain of the Ku proteins. These domains share a 7 stranded beta barrel. In the Ku proteins this domain interacts DNA, whereas the SPOC domain mediates protein binding.

The clan contains the following 4 members:

Ku Med25 Sld7_N SPOC

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
(210)
Full
(7775)
Representative proteomes UniProt
(24672)
RP15
(1060)
RP35
(3319)
RP55
(7052)
RP75
(11786)
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
(210)
Full
(7775)
Representative proteomes UniProt
(24672)
RP15
(1060)
RP35
(3319)
RP55
(7052)
RP75
(11786)
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
(210)
Full
(7775)
Representative proteomes UniProt
(24672)
RP15
(1060)
RP35
(3319)
RP55
(7052)
RP75
(11786)
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: Bateman A
Previous IDs: ku;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 210
Number in full: 7775
Average length of the domain: 192.2 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 40.03 %

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 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 204
Family (HMM) version: 19
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

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 Ku domain has been found. There are 58 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
A0A044SS53 View 3D Structure Click here
A0A044V532 View 3D Structure Click here
A0A077Z3N7 View 3D Structure Click here
A0A077Z6Y5 View 3D Structure Click here
A0A0D2DY03 View 3D Structure Click here
A0A0D2GBC7 View 3D Structure Click here
A0A0H5S0J9 View 3D Structure Click here
A0A0K0EJ46 View 3D Structure Click here
A0A0K0EJQ4 View 3D Structure Click here
A0A0N4UCA8 View 3D Structure Click here
A0A0N4UK87 View 3D Structure Click here
A0A0R0F6H1 View 3D Structure Click here
A0A0R4IB13 View 3D Structure Click here
A0A175VRH7 View 3D Structure Click here
A0A175W6D8 View 3D Structure Click here
A0A1C1CQF0 View 3D Structure Click here
A0A1C1CV14 View 3D Structure Click here
A0A1D6F8Z7 View 3D Structure Click here
A0A1D6LC75 View 3D Structure Click here
A0A1D8PF81 View 3D Structure Click here
A0A1D8PSH5 View 3D Structure Click here
A0A3P7DCJ0 View 3D Structure Click here
A0A3P7EDK8 View 3D Structure Click here
A0A3Q0KIK2 View 3D Structure Click here
A0A3Q0KV85 View 3D Structure Click here
A0A5K4EZ11 View 3D Structure Click here
A0A5K4EZY4 View 3D Structure Click here
A0A5S6PY80 View 3D Structure Click here
A0A5S6PYW0 View 3D Structure Click here
A0A7I4NNB8 View 3D Structure Click here
A0R3S7 View 3D Structure Click here
A4FFJ9 View 3D Structure Click here
A4FG06 View 3D Structure Click here
A4FQ42 View 3D Structure Click here
A4I4G4 View 3D Structure Click here
A4I561 View 3D Structure Click here
A4Z012 View 3D Structure Click here
A5G742 View 3D Structure Click here
A5G743 View 3D Structure Click here
A8HV31 View 3D Structure Click here