Journal: bioRxiv

Article Title: Cryo-EM structures of the CDK11-cyclin L-SAP30BP complex reveal mechanisms of CDK11 regulation

doi: 10.64898/2026.03.24.713564

Figure Lengend Snippet: ( a ) Bound AMP-PNP in the active site of CDK11 (green). Residues involved in interactions with the nucleotide are shown as sticks, hydrogen bonds are indicated as black dashed lines, and magnesium ions are shown as green spheres. ( b ) The pseudo-substrate density occupying the substrate binding site of CDK11 is shown in light green (CDK11 green, T-loop blue, SAP30BP yellow, cyclin L purple). ( c ) Cryo-EM map shown as grey mesh and semi-transparent surface, with fitted model coloured as in b. ( d ) Molecular model of the CDK11 pseudo-substrate segment (residues 751-762, light green) occluding the substrate binding site. ( e ) CDK2-cyclin A (cyan and yellow) in complex with a substrate peptide (sand) in the same view as panel C (PDB ID 3QHR) . ( f ) Kinase assay using an SF3B1 1-463 substrate and trimeric kinase complexes containing CDK11B p110 wild type (WT) and the 1-743, S752E, and S752A variants. SF3B1 phospho-T313 (P-T313) was detected using Western blot. A loading control stained with Ponceau S is provided. ( g ) Quantification of Western blot band intensities, presented as the mean ± standard deviation and individual data points of N = 4 kinase assay technical replicates. The relative activity of the wild-type complex at 60 min was set to 1. The significance level for activity comparisons between complexes, determined by 2-way ANOVA and Tukey’s multiple comparisons test, is provided (*: p < 0.05; **: p < 0.01). ( h ) Schematic illustration of the effect of pseudo-substrate phosphorylation on the efficiency of binding of a simple model substrate to CDK11. Hypothetical models for effects on substrate specificity in the context of more complex substrates are shown in Supplementary Fig. 4e, f. The substrate binding site is schematically represented as a cleft, and the active site is indicated by a stylised ATP molecule.

Article Snippet: CDK2 was expressed with an N-terminal His 10 -tag (Addgene plasmid #79726; http://n2t.net/addgene:79726 ; RRID:Addgene_79726, provided by John Chodera, Nicholas Levinson, and Markus Seeliger) , and cyclin A2 was expressed with an N-terminal His 6 -tag.

Techniques: Binding Assay, Cryo-EM Sample Prep, Kinase Assay, Western Blot, Control, Staining, Standard Deviation, Activity Assay, Phospho-proteomics

Journal: bioRxiv

Article Title: Cryo-EM structures of the CDK11-cyclin L-SAP30BP complex reveal mechanisms of CDK11 regulation

doi: 10.64898/2026.03.24.713564

Figure Lengend Snippet: ( a ) Rendering of CDK11-bound OTS964 (blue) in the cryo-EM map (shown as semi-transparent grey mesh and surface). ( b , c ) Active site views of the CDK11-cyclin L-SAP30BP-OTS964 complex in the two alternative conformations observed in the cryo-EM reconstruction. Hydrogen bonds (donor-acceptor distance 3.5 Å or less) are indicated by black dashed lines. The shortest distance between inhibitor and gatekeeper residue (M516 in CDK11) is indicated and shown by a white dashed line. The change in position of Y449 between panels b and c is indicated with a dashed arrow in panel b. ( d ) Comparison of the structure of CDK11-cyclin L-SAP30BP-OTS964 (CDK11 in green, cyclin L in purple with residues 173-181 in pink, OTS964 in blue) to the structure of isolated CDK11B-OTS964 (PDB ID 7UKZ ; light green and light blue, respectively). The site of steric incompatibility of the isolated CDK11B conformation with the presence of cyclin L is indicated by a black triangle. Shifts in adjacent loops because of cyclin binding are indicated by arrows. ( e ) Active site view of the CAK-OTS964 complex (CDK7 is shown in grey, water molecules as red spheres). Only the hydrogen bonds to the hinge region are preserved because several hydrogen bonding partners are absent or beyond hydrogen bonding distance (distance to D97 indicated by a yellow dashed line). The distance to the gatekeeper residue (F91 in CDK7) is enlarged (yellow dashed line). ( f ) Active site view of the CDK2-cyclin A2-OTS964 complex (CDK2 is shown in cyan). OTS964 forms three hydrogen bonds to CDK2, as it is within hydrogen bonding distance of CDK2 D86. Y15 is tucked under the dimethylamino-propyl group of OTS964.

Article Snippet: CDK2 was expressed with an N-terminal His 10 -tag (Addgene plasmid #79726; http://n2t.net/addgene:79726 ; RRID:Addgene_79726, provided by John Chodera, Nicholas Levinson, and Markus Seeliger) , and cyclin A2 was expressed with an N-terminal His 6 -tag.

Techniques: Cryo-EM Sample Prep, Residue, Comparison, Isolation, Binding Assay

Journal: Cell Death & Disease

Article Title: Dual targeting of PI3Kδ and PPARα enhances antitumor activity via FoxO1 activation in follicular lymphoma

doi: 10.1038/s41419-026-08593-5

Figure Lengend Snippet: A - C EdU flow plots for Karpas-422, RL, and Sc-1 cells after 24-h treatment (Linperlisib 32 μM; Chiglitazar 16 μM). D – F Quantification of EdU-positive cells showing reduced DNA synthesis with the combination ( n = 3). G – L ( G , H ) for Karpas-422; ( I , J ) for RL; ( K , L ) for Sc-1. Cell-cycle distribution by PI staining, demonstrating G0/G1 accumulation with Linperlisib and further enhancement by the combination (Linperlisib 16 μM; Chiglitazar 8 μM; n = 3). M GSEA indicating negative enrichment of the G1/S transition pathway (NES = − 2.85865, p < 0.00001). N – P Western blots of G1/S checkpoint proteins (p27, Cyclin E1, CDK2, p-CDK2); combination treatment increased p27 and decreased Cyclin E1, CDK2, and p-CDK2 (representative of three independent experiments).

Article Snippet: The primary antibodies used were as follows: PI3K p110δ (A19742; ABclonal), pan-Akt (#4691; CST), phospho-Akt (Ser473, #4060; CST), PPARα (ab227074; Abcam), FoxO1 (#2880; CST), phospho-FoxO1 (Thr24, #9464; CST) and (Ser256, #9461; CST), FoxO3a (#12829; CST), FoxO4 (#9472; CST), Mcl-1 (#16225-1-AP; Proteintech), Bcl-2 (#12789-1-AP; Proteintech), Bim (A19702; ABclonal), Bax (#50599-2-Ig; Proteintech), Cleaved PARP(#5625; CST), P21(#2947; CST), p27 (#3686; CST), Cyclin E1 (#11935-1-AP; Proteintech), CDK2 (#10122-1-AP; Proteintech), phospho-CDK2 (#4539; CST), GLUT1(#73015; CST), PGK1(A12686; ABclonal), β-Tubulin (#10094-1-AP; Proteintech), Lamin B1 (#13435; CST), and β-Actin (#66009-1-Ig; Proteintech).

Techniques: DNA Synthesis, Staining, Western Blot