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36  structures 822  species 0  interactions 953  sequences 17  architectures

Family: XLF (PF09302)

Summary: XLF-Cernunnos, XRcc4-like factor, NHEJ component

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XLF-Cernunnos, XRcc4-like factor, NHEJ component Provide feedback

XLF (also called Cernunnos) is Xrcc4-like-factor, and interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated down-regulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining [1]. This family contains Nej1 (non-homologous end-joining factor) [2] and Lif1, ligase-interacting factor [3]. XLF forms one of the components of the NHEJ machinery for DNA non-homologous end-joining [4].

Literature references

  1. Ahnesorg P, Smith P, Jackson SP; , Cell. 2006;124:301-313.: XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. PUBMED:16439205 EPMC:16439205

  2. Callebaut I, Malivert L, Fischer A, Mornon JP, Revy P, de Villartay JP; , J Biol Chem. 2006;281:13857-13860.: Cernunnos interacts with the XRCC4 x DNA-ligase IV complex and is homologous to the yeast nonhomologous end-joining factor Nej1. PUBMED:16571728 EPMC:16571728

  3. Dore AS, Furnham N, Davies OR, Sibanda BL, Chirgadze DY, Jackson SP, Pellegrini L, Blundell TL; , DNA Repair (Amst). 2005; [Epub ahead of print]: Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode. PUBMED:16388993 EPMC:16388993

  4. Riballo E, Woodbine L, Stiff T, Walker SA, Goodarzi AA, Jeggo PA;, Nucleic Acids Res. 2009;37:482-492.: XLF-Cernunnos promotes DNA ligase IV-XRCC4 re-adenylation following ligation. PUBMED:19056826 EPMC:19056826

  5. Li Y, Chirgadze DY, Bolanos-Garcia VM, Sibanda BL, Davies OR, Ahnesorg P, Jackson SP, Blundell TL;, EMBO J. 2008;27:290-300.: Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ. PUBMED:18046455 EPMC:18046455


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015381

XLF (also called Cernunnos) is involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. XLF and XRCC4 form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair [ PUBMED:23442139 ]. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated downregulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining [ PUBMED:16439205 ]. XLF is homologous to the yeast non-homologous end-joining factor Nej1 [ PUBMED:16571728 ]. This family contains Nej1 (non-homologous end-joining factor) and Lif1.

Gene Ontology

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Domain organisation

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Alignments

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(76)
Full
(953)
Representative proteomes UniProt
(1758)
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(127)
RP35
(350)
RP55
(651)
RP75
(960)
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  Seed
(76)
Full
(953)
Representative proteomes UniProt
(1758)
RP15
(127)
RP35
(350)
RP55
(651)
RP75
(960)
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  Seed
(76)
Full
(953)
Representative proteomes UniProt
(1758)
RP15
(127)
RP35
(350)
RP55
(651)
RP75
(960)
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.

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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: manual
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mistry J , Wood V , Hentges P, Doherty A
Number in seed: 76
Number in full: 953
Average length of the domain: 168.00 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 39.35 %

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 28.0 28.0
Trusted cut-off 28.1 28.0
Noise cut-off 27.9 27.9
Model length: 180
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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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 XLF domain has been found. There are 36 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