Table 2

Cyclin interactions of CDK9 identified by IP-MSa

Bait proteinCell lineNo. of unique peptides/total no. of peptides (X!Tandem score)
CDK9Cyclin:
K1/K2T1T2
Endogenous CDK9HEK29313/18 (−108.5)018/34 (−169.3)0
HeLaS315/17 (−118.9)04/4 (−27.2)0
3×FLAG-CDK9HEK293A13/27 (−116.2)03/3 (−18.4)0
CDK9-3×FLAGHEK293A15/31 (−145.4)011/13 (−98.8)0
HEK293A23/96 (−227)1/1 (−1.4)12/12 (−98.7)1/3 (−18.2)
  • a Endogenous CDK9 and N-terminally (3×FLAG-CDK9) and C-terminally tagged (CDK9-3×FLAG) proteins were immunoprecipitated, and the complex was analyzed for cyclin proteins.