2024-05-01 REL PDBe PDBe PDBe 2020-12-05 2021-02-10 2021-02-10 2024-05-01 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM127018 United States Cryo-EM structure of the human CAK bound to ICEC0942 at 2.5 Angstroms resolution Greber BJ Remis J Kinase, protein complex, small molecules inhibitor, CDK-activating kinase, TRANSCRIPTION Greber BJ Remis J Ali S Nogales E 2.5 angstrom -resolution structure of human CDK-activating kinase bound to the clinical inhibitor ICEC0942. Biophys.J. US 120 677 686 2021 33476598 doi:10.1016/j.bpj.2020.12.030 1542-0086 0030 BIOJAU EMD-11823 other EM volume EMD-11828 other EM volume 7b5o FULLOVERLAP CDK-activating kinase (CAK) in complex with ICEC0942 CDK-activating kinase (CAK) in complex with ICEC0942 0 1 2 3 Homo sapiens 0.12 CDK-activating kinase assembly factor MAT1 Homo sapiens 0.038132339999999994 1 Trichoplusia ni LEVO MGSSHHHHHHENLYFQSNAMDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQ LFEDPTVDKEVEIRKKVLKIYNKREEDFPSLREYNDFLEEVEEIVFNLTNNVDLDNTKKKMEIYQKENKDVIQKNKLKLT REQEELEEALEVERQENEQRRLFIQKEEQLQQILKRKNKQAFLDELESSDLPVALLLAQHKDRSTQLEMQLEKPKPVKPV TFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQDLAGGYTSSLACHRALQDAF SGLFWQPS P51948 Cyclin-H Homo sapiens 0.03769547299999999 1 Trichoplusia ni LEVO MYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAMPRSVV GTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIV HNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKE NRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYVSKKSKHEEEEWTDDDLV ESL P51946 Cyclin-dependent kinase 7 Homo sapiens 0.04365107 1 Trichoplusia ni LEVO MASWSHPQFEKGGGSGGGSGGGSWSHPQFEKSGGGSENLYFQSNAMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTN QIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIK AYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVD MWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGL FLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF P50613 2.7.11.22 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol 0.000394513 1 I74 water 1.8015e-05 73 HOH singleParticle particle 0.2 7.9 20.0 HEPES-KOH 200.0 KCl Potassium chloride 2.0 MgCl2 Magnesium chloride 5.0 beta-mercaptoethanol 1.0 Glycerol UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY PLASMA CLEANING AIR ETHANE-PROPANE 100 278 FEI VITROBOT MARK IV
Incubated with 50 uM ICEC0942 for 5 min
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.5 1.5 72886.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 3571 2.0 69.0
Movies (69 frames) acquired in 3 x 3 pattern by image shift
 GATAN K3 (6k x 4k) 2 5302 2.0 69.0
Movies (70 frames) acquired in 3 x 3 pattern by image shift
 1 10904715 EMD-22123 2 C1 FOURIER SPACE 2.5 FSC 0.143 CUT-OFF RELION 3.1 205478 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 4 180000.0 RELION 3.1
High-resolution, masked classification using 4 classes each for two datasets. One class from each dataset was selected, and the datasets were merged.
 emd_12042.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 131.712 131.712 131.712 90.0 90.0 90.0 X Y Z -0.13677126 0.26206034 -0.000028703422 0.013377107 1.029 1.029 1.029 0.045 AUTHOR Post-processed (sharpened, filtered) cryo-EM map, re-boxed into a 128 x 128 x 128 pixel box 6XBZ PDB experimental model RIGID BODY FIT
Real space refinement in PHENIX; ligand coordinates from PHENIX-OPLS3e refinement
REAL emd_12042_msk_1.map emd_12042_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 263.424 263.424 263.424 90.0 90.0 90.0 X Y Z -0.06432993 0.13440199 0.0000071475274 0.003799916 1.029 1.029 1.029 AUTHOR Unfiltered half-map emd_12042_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 263.424 263.424 263.424 90.0 90.0 90.0 X Y Z -0.06038004 0.14010051 0.0000065109093 0.0037609274 1.029 1.029 1.029 AUTHOR Unfiltered half-map