ELM candidate motifs
ELM annotation process is a tedious and time-consuming process involving critical reading of primary and secondary literature, finding motif instances,
generating multiple sequence alignments and more.
In order not to loose track of possible annotations, we keep the following list of candidate motifs.
We invite researchers to send us their feedback and expert opinion on these
classes and to contribute novel motif classes that will be added to the candidate page and ultimately be turned into full ELM classes.
Minimum requirements are at least one literature reference as well as a short description. In addition, a draft regular expression or a 3D structure showing the relevant interaction would also be helpful.
Currently 18 candidates need annotation: (Add a new candidate)
Detailed Status:| undergoing annotation: | 18 |
| Identifier | Model | References | Description | Notes | Status | |
|---|---|---|---|---|---|---|
| LIG_RCD1_1 | [DE].{1,2)}[YF].{1,4}[DE]L | PMID:27881680 PMID:25348421 | Motif in plant transcription factors binding to stress-associated plant protein Radical-induced Cell Death 1 (RCD1) |
undergoing annotation |
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| LIG_SH3_8 | [RK]..[RK] | PMID:12176364 PDB:1H3H PMID:15483625 | non canonical SH3 binding motif | confers specificity for the interaction between Gads and SLP-76 in T cell signaling. PMID:12176364 analyses the binding using short peptides. SLP-76 contains two R..K motifs, but only the first (PSIDRSTK) binds, the second (TFPSRSTK) does not (or wasn't done) |
undergoing annotation |
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| LIG_PUB_PIM_1 | DDDLY. | PMID:24726323 PMID:24726327 PDB:4OYK PDB:4P0A PDB:4P0B | Motif in OTULIN/Fam105B binding to the PUB domain of the HOIP protein, part of the LUBAC complex, a generator of Met1-linked ubiquitin chains. Similar motif in P97 binds more weakly and also binds to PLAA PUL domain (see LIG_PUL_PLAA_1 candidate) |
undergoing annotation |
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| LIG_PLK_PoloBox_1 | #.S([ST]).. | PMID:12595692,PMID:14532005 | Phosphoserine site recognised by the Polo-like-kinase via the Polo Boxes. The pSer-peptide binds along the groove between the two Polo boxes |
undergoing annotation |
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| LIG_PH_Tfb1 | [ILVF]..W[ILVF].[DE] | PMID:16793543,PDB:2GS0 | Amphipathic helix motif in P53 that is recognised by the PH domain of the p62 subunit of TFIIH. 3uM and phosphorheostatic binding (pS46 518nM, pT55 457nM and pS46pT55 97nM). |
undergoing annotation |
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| LIG_Rrp6Rrp47_Mtr4_1 | [DE]LFx[VC]F[ED]{1,2} | PMID:25319414 PDB:4WFD | Exosome associated Rrp6 and Rrp47 modules associate by mutual induced fit into a six-helical intertwined heterodimeric folded domain. The N-terminal helical motif of TRAMP complex factor Mtr4 binds in a surface groove of the preassembled Rrp6-Rrp47 fold. In this way, the TRAMP complex can dock to the exosome as part of its RNA processing function. |
undergoing annotation |
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| LIG_FAT_Reverse | L..L[LM] | PMID:18078954,PDB:3B71 | Motif in CD4 used to bind FAT domain of Focal Adhesion Kinase. Binds the same binding surface as the similarly hydrophobic helical LD motifs of Paxillin but has an anti parallel orientation. |
undergoing annotation |
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| LIG_CDC20_ABBA_1 | [FIVL].[ILMVP][FHY].[DE].{0,3}[DEST] | PMID:25669885, PMID:23707760, PDB:4bh6 | The ABBA motif binds the CDC20/CDH1 coactivator subunit of the anaphase promoting complex. It is found in a number of key cell cycle proteins. In yeast ACM1, ABBA acts cooperatively with KEN and D-Box motifs to inhibit the APC. It is likely to function similarly in metazoan BubR1. In metazoan cyclin A, the ABBA acts as a degron enabling the cyclin’s destruction in prometaphase, while the APC is otherwise not yet active. |
undergoing annotation |
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| LIG_BART_Arl2_1 | LL[^p][^p]L[^p][^p]LK | PMID:19368893, PDB:3DOE | In the GTP bound form, the small GTPase Arl2 expels its N-terminal helix which becomes available to bind the BART domain of BART protein. The Arl2 molecular switching system regulates transport of farnesylated proteins. |
undergoing annotation |
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| LIG_CaM_NSCaTE_1 | W[^P][^P][^P][IL][^P][AGS][AT] | PMID:23626724, PMID:22518098, PMID:18235447, PMID:22518098, PDB:2LQC | Helical motif binding to Calmodulin. Found in N-termini of some calcium channels (CaV1.2/CaV1.3). Presence in long isoforms dependent on alternative translation start. Involved in channel function. Different from the classical Lig_IQ Calmodulin-binding motif. |
undergoing annotation |
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| LIG_LSD1_SNAG_1 | ^mPRsFLv[KR]k | PMID:20389281, PMID:21300290, PDB:2Y48 | The SNAG domain is a conserved N-terminal motif in some zinc finger and homeobox TFs such as SNAIL, Scratch, GFI1, Gsx1. Inhibits LSD1 demethylation of H3K4 by competitive inhibition of the active site. Has repressive effect. |
undergoing annotation |
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| MOD_Chk_1 | L.R..[ST]. or L.P..[ST]F | PMID:12711320, PMID:11821419, PMID:15279791 | Several basophilic kinases are reported to have additional hydrophobic residue preferences, including CHK1,2, MK2, PKD. LxRXX(ST) is one such variant p-site motif. Also the +1 position is often hydrophobic. In the case of CHK2, the R can be replaced by P (as in BRCA-1) but then the other positions must be optimal as in LxPxxSF. Therefore it appears that some flexibility in the 3 specificity residues is possible, where, if one position is poor, the others must be optimal. |
undergoing annotation |
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| DCK_phos_PKA_1 | [ILMVFA][ILMVFA]..[ILMVFA]...[ILMVFA][ILMVFA]..[ILMVFA] | PMID:20159461, PDB:3IM4 | Large amphipathic hydrophobic docking motif for RI and RII regulatory subunits of cyclic AMP dependent protein kinase (PKA). Binds to the D/D dimerisation/docking domain. Found in most AKAP proteins. |
undergoing annotation |
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| Mod_CDK_Long_2 | ...[SP]..K | PMID:21712545 | Longer version of the cyclin/CDK phosphosite recognised by e.g. CDK1. Lysine is specific in the charge position. |
undergoing annotation |
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| MOD_HedgehogLipid | PMID:9593755,PMID:11486055,PMID:11493554 | Keeps Hedgehog attached to plasma membrane for short range extracellular signalling. Probably needs its own functional site and different ELM entries. |
undergoing annotation |
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| LIG_WW_Itch | PP.Y....[ST][ILV] | PMID:20855944 | Extended WW domain binding motif necessary for binding to the 2nd WW domain of Itch. Mutations in the final hydrophobic position have been shown to reduce binding and have been implicated in both Hays-Wells syndrome and Rapp Hodgkin syndrome. |
undergoing annotation |
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| LIG_WW_Fe65 | PPLA | PMID:18547980 | Putative motif claimed for GSK3beta for binding to Fe65. This interaction is posited to regulate apoptosis and phosphorylation of Tyr 216 of GSK3beta. | The sequence region is post-kinase domain but is structured. The PPLA sequence is very poorly conserved too... |
undergoing annotation |
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| LIG_Centrin_XPC | W..L...[IL] | PMID:15964821 | Motif responsible for the binding of XPC repair protein to Centrin 2. PDB structures available. |
undergoing annotation |
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Please cite:
ELM-the Eukaryotic Linear Motif resource-2024 update.
(PMID:37962385)
ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement
ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement