2025-07-09 REL PDBe INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBe PDBe 2024-02-14 2024-12-25 2024-12-25 2025-07-09 Not funded Cryo-EM structure of CAK in complex with SY-5609 Feng J Cronin NB Marineau JJ Greber BJ Kinase, covalent inhibitor, transcription, cell cycle Jones T Feng J Luyties O Cozzolino K Sanford L Rimel JK Ebmeier CC Shelby GS Watts LP Rodino J Rajagopal N Hu S Brennan F Maas ZL Alnemy S Richter WF Koh AF Cronin NB Madduri A Das J Cooper E Hamman KB Carulli JP Allen MA Spencer S Kotecha A Marineau JJ Greber BJ Dowell RD Taatjes DJ TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network. Sci Adv US 11 eadr9660 eadr9660 2025 40020069 doi:10.1126/sciadv.adr9660 2375-2548 EMD-19627 other EM volume 8s0t FULLOVERLAP CDK-activating kinase CDK-activating kinase 0 1 2 3
Human CAK bound to the non-covalent inhibitor SY-5609
Homo sapiens 0.085 CDK-activating kinase assembly factor MAT1 Homo sapiens 0.010234531 1 Trichoplusia ni LEVO SNAPVTFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQDLAGGYTSSLACHRA LQDAFSGLFWQPS P51948 Cyclin-H Homo sapiens 0.037721508 1 Trichoplusia ni LEVO (ACE)MYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYYEKRLLEFCSVFKPAM PRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLN FHLIVHNPYRPFEGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSES LMLKENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYVSKKSKHEEEEWT DDDLVESL P51946 Cyclin-dependent kinase 7 Homo sapiens 0.039362598 1 Trichoplusia ni LEVO SNAMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGL LDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFG LAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQW PDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETL KEQSNPALAIKRKRTEALEQGGLPKKLIF P50613 2.7.11.22 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile 0.000490461 1 YNK water 1.8015e-05 145 HOH singleParticle particle 0.3 7.9 20.0 HEPES-KOH 250.0 KCl potassium chloride 2.0 MgCl2 magnesium chloride 5.0 beta-mercaptoethanol 0.7 glycerol
Buffer contained 54 uM inhibitor SY-5609.
 UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY PLASMA CLEANING
Tergeo EM plasma cleaner
 ETHANE 100 278 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.4 1.8 96153.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 2 14170 70.0 1 RELION 4.0 beta cryoSPARC v3.3.1 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-22123 2.3 FSC 0.143 CUT-OFF RELION 4.0 beta 151410 MAXIMUM LIKELIHOOD RELION 4.0 beta MAXIMUM LIKELIHOOD RELION 4.0 beta RELION 4.0 beta emd_19628.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 0 0 0 224 224 224 193.76001 193.76001 193.76001 90.0 90.0 90.0 X Y Z -0.07322119 0.10982158 0.000009313999 0.003540422 0.86500007 0.86500007 0.86500007 0.02 AUTHOR Post-processed (sharpened, filtered) cryo-EM map 8ORM PDB experimental model RIGID BODY FIT REAL emd_19628_msk_1.map emd_19628_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 0 0 0 224 224 224 193.76001 193.76001 193.76001 90.0 90.0 90.0 X Y Z -0.032114808 0.0623971 0.000009164023 0.0022070396 0.86500007 0.86500007 0.86500007 AUTHOR Half map emd_19628_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 0 0 0 224 224 224 193.76001 193.76001 193.76001 90.0 90.0 90.0 X Y Z -0.033064045 0.060027782 0.000009463975 0.0021676186 0.86500007 0.86500007 0.86500007 AUTHOR Half map