9HIY: CAK

Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with ATPgS. Determined by electron microscopy at 2.3 Å resolution. Released 20 Aug 2025.

Method
Electron microscopy
Resolution
2.3 Å
Organism
Homo sapiens
Chains
3
Atoms
5,103
Mol. weight
87.87 kDa
Ligands
MG, AGS
Released
20 Aug 2025

Explore 9HIY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HIY contains 39 α-helices and 11 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 5 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix266-2694
α-helix271-2744
α-helix276-2794
α-helix280-2856
α-helix289-30113
Chain I: 19 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-43
α-helix6-105
α-helix16-3520
α-helix50-7021
α-helix74-763
α-helix77-9216
α-helix101-11515
α-helix122-1287
α-helix134-15320
α-helix164-17714
α-helix184-1863
α-helix189-20012
α-helix203-2053
α-helix209-22315
α-helix229-2302
α-helix231-2355
α-helix242-26019
α-helix264-2663
α-helix267-28014
Chain J: 15 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand12-2091
β-strand24-3181
β-strand36-4381
α-helix57-6610
β-strand7412
β-strand77-8151
β-strand88-9251
β-strand96-9722
α-helix98-1036
α-helix111-13020
β-strand133-13423
α-helix140-1423
β-strand143-14532
β-strand151-15332
β-strand160-16123
α-helix176-1783
α-helix181-1844
α-helix193-20816
α-helix218-22912
α-helix240-2423
α-helix257-2604
α-helix266-27510
α-helix286-2905
α-helix293-2964
α-helix300-3034
α-helix304-3063

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
CDK-activating kinase assembly factor MAT1Hprotein93Homo sapiensP51948 (AlphaFold model)
Cyclin-HIprotein324Homo sapiensP51946 (AlphaFold model)
Cyclin-dependent kinase 7Jprotein349Homo sapiensP50613 (AlphaFold model)
Sequence of entity 1 (H), FASTA
>9HIY_1 CDK-activating kinase assembly factor MAT1 (chains H)
SNAPVTFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVR
AASPQDLAGGYTSSLACHRALQDAFSGLFWQPS
Sequence of entity 2 (I), FASTA
>9HIY_2 Cyclin-H (chains I)
XMYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKY
YEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFN
VSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP
ILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLK
ENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYED
DDYVSKKSKHEEEEWTDDDLVESL
Sequence of entity 3 (J), FASTA
>9HIY_3 Cyclin-dependent kinase 7 (chains J)
SNAMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINR
TALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETNLEVIIKDNSLVLTPSHIKAY
MLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRW
YRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQW
PDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSN
RPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1
AGSPhosphothiophosphoric acid-adenylate esterC10 H16 N5 O12 P3 S1

Primary citation

Resistance to CDK7 inhibitors directed by acquired mutation of a conserved residue in cancer cells. Lai, C.F., Cushing, V.I., Olden, E. et al. EMBO J (2025) 44:5860-5889. DOI 10.1038/s44318-025-00554-6 · PubMed

Other PDB entries of the same protein (UniProt P51948 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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