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TitleHigh-throughput investigation of cyclin docking interactions reveals the complexity of motif binding determinants.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 7622, Year 2025
Publish dateAug 15, 2025
AuthorsMihkel Örd / Matthew J Winters / Mythili S Subbanna / Natàlia de Martín Garrido / Victoria I Cushing / Johanna Kliche / Caroline Benz / Ylva Ivarsson / Basil J Greber / Peter M Pryciak / Norman E Davey /
PubMed AbstractMany regulatory protein-protein interactions depend on Short Linear Motifs (SLiMs). In the cell cycle, cyclin-CDKs recognize SLiMs to control substrate recruitment and phosphorylation timing. Here, ...Many regulatory protein-protein interactions depend on Short Linear Motifs (SLiMs). In the cell cycle, cyclin-CDKs recognize SLiMs to control substrate recruitment and phosphorylation timing. Here, we measure the relative binding strength of ~100,000 peptides to 11 human cyclins from five families (D, E, A, B, and F). Using a quantitative intracellular binding assay and large-scale tiled peptide screening, we identify multiple non-canonical binders unveiling a broader repertoire of cyclin docking motif types. Cryo-electron microscopy and saturation mutagenesis studies reveal distinct binding modes and sequence features governing motif recognition, binding strength, and cyclin preference. Docking motifs vary from highly selective to pan-cyclin, thereby fine-tuning the timing of CDK phosphorylation during cell cycle. Overall, these findings provide insights into the rules encoding specificity and affinity of SLiM-mediated interactions and offer a framework for understanding motif-driven protein networks across the proteome.
External linksNat Commun / PubMed:40817109 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.2 Å
Structure data

52201

9hiu

EMDB-52201, PDB-9hiu:
Cryo-EM structure of CDK2-cyclin A bound to a GMNC peptide
Method: EM (single particle) / Resolution: 3.2 Å

52204

9hiw

EMDB-52204, PDB-9hiw:
Cryo-EM structure of CDK2-cyclin A bound to a SAMHD1 peptide
Method: EM (single particle) / Resolution: 3.1 Å

52208

9hj1

EMDB-52208, PDB-9hj1:
Cryo-EM structure of CDK2-cyclin A bound to a SCAPER peptide
Method: EM (single particle) / Resolution: 2.9 Å

Source
  • homo sapiens (human)
KeywordsCELL CYCLE / Kinase / cyclin / short linear motif / cdk2 / cyclin A

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