8BYA

Cryo-EM structure of SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex

Summary for 8BYA

• Entry DOI: 10.2210/pdb8bya/pdb
• EMDB information: 16325
• Descriptor: Cyclin-dependent kinase 2, Cyclin-A2, Cyclin-dependent kinase inhibitor 1B, ... (7 entities in total)
• Functional Keywords: cell cycle, cyclin-dependent kinase, signalling, ubiquitination
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 7
• Total formula weight: 177585.62

Authors

Rowland, R.J.,Salamina, M.,Endicott, J.A.,Noble, M.E. (deposition date: 2022-12-12, release date: 2023-06-28, Last modification date: 2024-11-20)

Primary citation

Rowland, R.J.,Heath, R.,Maskell, D.,Thompson, R.F.,Ranson, N.A.,Blaza, J.N.,Endicott, J.A.,Noble, M.E.M.,Salamina, M.
Cryo-EM structure of SKP1-SKP2-CKS1 in complex with CDK2-cyclin A-p27KIP1.
Sci Rep, 13:10718-10718, 2023

PubMed Abstract: p27KIP1 (cyclin-dependent kinase inhibitor 1B, p27) is a member of the CIP/KIP family of CDK (cyclin dependent kinase) regulators that inhibit cell cycle CDKs. p27 phosphorylation by CDK1/2, signals its recruitment to the SCF (S-phase kinase associated protein 1 (SKP1)-cullin-SKP2) E3 ubiquitin ligase complex for proteasomal degradation. The nature of p27 binding to SKP2 and CKS1 was revealed by the SKP1-SKP2-CKS1-p27 phosphopeptide crystal structure. Subsequently, a model for the hexameric CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex was proposed by overlaying an independently determined CDK2-cyclin A-p27 structure. Here we describe the experimentally determined structure of the isolated CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex at 3.4 Å global resolution using cryogenic electron microscopy. This structure supports previous analysis in which p27 was found to be structurally dynamic, transitioning from disordered to nascent secondary structure on target binding. We employed 3D variability analysis to further explore the conformational space of the hexameric complex and uncovered a previously unidentified hinge motion centred on CKS1. This flexibility gives rise to open and closed conformations of the hexameric complex that we propose may contribute to p27 regulation by facilitating recognition with SCF. This 3D variability analysis further informed particle subtraction and local refinement approaches to enhance the local resolution of the complex.

PubMed: 37400515
DOI: 10.1038/s41598-023-37609-9

Experimental method

ELECTRON MICROSCOPY (3.38 Å)