The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Ligand motif binding the CSL BTD
Functional site description:
The DNA binding β-trefoil domain is built out of a capped β-barrel, which has an internal pseudo threefold symmetry. In CSL proteins this domain functions as an interaction site for NotchIC (the intracellular post-proteolytic part of the Notch receptor), co-repressors and some viral regulatory proteins such as EBNA2 and EBNA3. CSL (CBF1/RBP-j𝜅, Su(H), Lag-1) proteins serve as co-repressors or as co-activators of Notch pathway target gene expression. CSL’s regulatory character changes from a repressing to an activating component when the RAM domain of NotchIC binds to it. This interaction with NotchIC is necessary for the expression of genes that are important in embryonic developmental processes and tissue maintenance.
ELM Description:
The ɸWɸP motif represents the main interaction site between Notch-like proteins and CSL transcription factors. This interaction plays an important role in the Notch pathway. The very conserved W and P in the CSL binding-motif enter into a hydrophobic pocket provided by CSL(Wilson,2006).The other two positions are less conserved but both also have hydrophobic preferences. Since CSL may function as either a gene expression repressor or activator, depending on it’s conformation, it represents a key step in gene expression where several co-regulatory proteins operate. RITA and KyoT2 are such co-regulators and interact with CSL via the same binding motif as Notch, ɸWɸP (Wacker,2011; Collins,2014).
Some viruses have developed mechanisms to manipulate Notch-signalling by expressing proteins that carry this binding motif and thus permanently stimulate Notch-like expression regulation (Calderwood,2011; Heinzelmann,2010).
In all non-viral proteins, which carry the motif, a conserved occurrence of a G or an A at least 3 positions in front of the SLiM can be noticed. In Notch proteins, a basic region of circa five amino acids length precedes the hydrophobic motif, separated by a gap of about five residues. The basic residues also bind to CSL.
The viral proteins, which tend to manipulate Notch-controlled gene-expression, do not show these extra residues, having just the core WxP-based motif. Often the viral proteins have multiple WxP motifs, some of which do not match the ELM pattern, having a non-hydrophobic residue in the less conserved positions. It is likely that the viral motifs can bind multiple CSL molecules.
Pattern Probability: 0.0001278
Present in taxons: Metazoa Viruses
Interaction Domain:
BTD (PF09270) Beta-trefoil DNA-binding domain (Stochiometry: 1 : 1)
o See 18 Instances for LIG_CSL_BTD_1
o Abstract
In metazoa, the highly conserved Notch pathway plays an important role in embryonic development, cell fate determination, and maintenance processes. When the single-pass transmembrane Notch receptor binds to its ligand, Delta, a membrane-bound protein of neighbouring cells, three proteolytic cleavages take place and lead to the release of NotchIC, the intracellular domain and effector of Notch (18363556).NotchIC then translocates into the nucleus and regulates transcription of target genes by recruiting cofactors and assembling with them into the regulation-complex. The complex consists of intracellular Notch, the co-activating protein, Mastermind, and the transcription factor CSL (CBF1/RBPj𝜅; Su(H); Lag-1 20972443). In the complex, the β-trefoil domain (BTD) of CSL interacts with the RBPJ-associated molecule (RAM) intrinsically disordered domain (IDD) of the Notch protein.
This interaction is mainly managed by a short hydrophobic xWxP amino acid sequence in the Notch like proteins(Notch1, P46531; Notch2, Q04721; Notch3, Q9UM47; Notch4, Q99466; Lin-12, P14585; GLP1, P13508), which is highly conserved across species. In the complex, the W and P of the motif are directed into a hydrophobic pocket of the CSL BTD domain (Wilson,2006, 2FO1).
CSL also interacts with the corepressor KyoT2, A2AEX7 (Collins,2014) and RITA, RBP-J interacting and tubulin associated, P0CJ62 (Wacker,2011) via this motif. RITA exports CSL from the nucleus. Ataxin1, P5253 (Tong,2011) may also have the motif, though it has not been shown to be functional.
EBNA2, Q3KSV2 (Calderwood,2011); EBNA3, Q3KST2 (Calderwood,2011); EBNA6, P03204 (8627785) and K10, F5H9D8 (Heinzelmann,2010) are viral proteins that bind to CSL and thus take effect on gene-regulation of Notch-target genes. The viral proteins often have repeated xWxP motifs, suggesting that they bind multiple copies of CSL.
o 8 selected references:

o 13 GO-Terms:

o 18 Instances for LIG_CSL_BTD_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q6AW86 ZNF324B
59 62 IQLERGEEPWVPSGKDMTLA TP 2 Homo sapiens (Human)
P03204 EBNA6
96 99 LDTEDNVPPWLPPHDITPYT TP 2 Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
772 775 LHQPPMEGPWVPEQWMFQGA TP 6 Human herpesvirus 4 (Epstein-Barr virus)
583 586 ARERWRPAPWTPNPPRSPSQ TP 6 Human herpesvirus 4 (Epstein-Barr virus)
289 292 HHLPSGPPWWPPICDPPQPS TP 6 Human herpesvirus 4 (Epstein-Barr virus)
P0CJ62 rita1
142 145 DTVKIRPLLWSPSPRLVQQS TP 6 Xenopus laevis (African clawed frog)
P0CJ62 rita1
70 73 APPSQTPLLWSPGEIKENKK TP 6 Xenopus laevis (African clawed frog)
A2AEX7 Fhl1
190 193 NKGLVKAPVWWPMKDNPGTT TP 3 Mus musculus (House mouse)
P13508 glp-1
803 806 KRKMVNATVWMPPMESTNEK TP 1 Caenorhabditis elegans
F5H9D8 vIRF-4
203 206 TEQKAACSVWIPVNEGASTS TP 2 Human herpesvirus 8
P46531 NOTCH1
1767 1770 KRRRQHGQLWFPEGFKVSEA TP 4 Homo sapiens (Human)
P54253 ATXN1
44 47 DNHRVEGTAWLPGNPGGRGH TP 1 Homo sapiens (Human)
F5H9D8 vIRF-4
487 490 VVPEVRTPLWIPWSSGGAPN TP 2 Human herpesvirus 8
F5H9D8 vIRF-4
306 309 GSRLPSTSPWIPACFPWGDL TP 2 Human herpesvirus 8
P14585 lin-12
944 947 KRRMINASVWMPPMENEEKN TP 2 Caenorhabditis elegans
Q99466 NOTCH4
1481 1484 RRRREHGALWLPPGFTRRPR TP 1 Homo sapiens (Human)
1674 1677 RRKREHSTLWFPEGFSLHKD TP 1 Homo sapiens (Human)
Q04721 NOTCH2
1709 1712 KRKRKHGSLWLPEGFTLRRD TP 1 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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