9SKQ: CAK-CDK1-cyclin B1
Cryo-EM structure of CAK-CDK1-cyclin B1. Determined by electron microscopy at 3.4 Å resolution. Released 15 Oct 2025.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 9,750
- Mol. weight
- 203.99 kDa
- Ligands
- MG, ANP
- Released
- 15 Oct 2025
Explore 9SKQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9SKQ contains 72 α-helices and 25 β-strands across 5 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 A: 14 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-11 | 6 | 5 |
| β-strand | 18-22 | 5 | 5 |
| β-strand | 29-36 | 8 | 5 |
| α-helix | 46-57 | 12 | |
| β-strand | 63 | 1 | 6 |
| β-strand | 68 | 1 | 5 |
| β-strand | 75-80 | 6 | 5 |
| β-strand | 85-86 | 2 | 6 |
| α-helix | 87-93 | 7 | |
| α-helix | 95 | 1 | |
| α-helix | 102-121 | 20 | |
| β-strand | 124-125 | 2 | 7 |
| α-helix | 131-133 | 3 | |
| β-strand | 134-136 | 3 | 6 |
| β-strand | 142-144 | 3 | 6 |
| β-strand | 151-152 | 2 | 7 |
| α-helix | 157-159 | 3 | |
| α-helix | 172-175 | 4 | |
| α-helix | 185-199 | 15 | |
| α-helix | 209-220 | 12 | |
| α-helix | 250-253 | 4 | |
| α-helix | 258-267 | 10 | |
| α-helix | 276-277 | 2 | |
| α-helix | 278-281 | 4 | |
| α-helix | 285-287 | 3 | |
Chain B: 17 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 171-184 | 14 | |
| α-helix | 199-215 | 17 | |
| α-helix | 220-234 | 15 | |
| α-helix | 241-243 | 3 | |
| α-helix | 244-259 | 16 | |
| α-helix | 266-271 | 6 | |
| α-helix | 281-293 | 13 | |
| α-helix | 302-312 | 11 | |
| α-helix | 317-330 | 14 | |
| α-helix | 341-355 | 15 | |
| α-helix | 363-365 | 3 | |
| α-helix | 366-369 | 4 | |
| α-helix | 377-391 | 15 | |
| α-helix | 398-401 | 4 | |
| α-helix | 412-414 | 3 | |
| α-helix | 416-419 | 4 | |
| α-helix | 421-428 | 8 | |
Chain H: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 264-266 | 3 | |
| α-helix | 272-274 | 3 | |
| α-helix | 276-279 | 4 | |
| α-helix | 280-285 | 6 | |
| α-helix | 289-300 | 12 | |
Chain I: 17 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| α-helix | 16-37 | 22 | |
| α-helix | 50-68 | 19 | |
| α-helix | 74-76 | 3 | |
| α-helix | 77-92 | 16 | |
| α-helix | 101-115 | 15 | |
| α-helix | 122-128 | 7 | |
| α-helix | 133-153 | 21 | |
| α-helix | 164-177 | 14 | |
| α-helix | 184-187 | 4 | |
| α-helix | 188-200 | 13 | |
| α-helix | 203-205 | 3 | |
| α-helix | 209-223 | 15 | |
| α-helix | 229-230 | 2 | |
| α-helix | 231-235 | 5 | |
| α-helix | 242-261 | 20 | |
| α-helix | 267-281 | 15 | |
Chain J: 19 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 13 | 1 | 1 |
| β-strand | 19-20 | 2 | 1 |
| β-strand | 24-30 | 7 | 1 |
| β-strand | 37-43 | 7 | 1 |
| α-helix | 44 | 1 | |
| α-helix | 57-66 | 10 | |
| β-strand | 74 | 1 | 2 |
| β-strand | 77-79 | 3 | 1 |
| β-strand | 82 | 1 | 3 |
| β-strand | 87 | 1 | 3 |
| β-strand | 88-92 | 5 | 1 |
| β-strand | 96-97 | 2 | 2 |
| α-helix | 98-103 | 6 | |
| α-helix | 111-130 | 20 | |
| β-strand | 133-134 | 2 | 4 |
| α-helix | 140-142 | 3 | |
| β-strand | 143-145 | 3 | 2 |
| β-strand | 152-153 | 2 | 2 |
| α-helix | 156-158 | 3 | |
| β-strand | 160-161 | 2 | 4 |
| α-helix | 176-178 | 3 | |
| α-helix | 181-185 | 5 | |
| α-helix | 193-208 | 16 | |
| α-helix | 218-229 | 12 | |
| α-helix | 231-233 | 3 | |
| α-helix | 234-236 | 3 | |
| α-helix | 240-242 | 3 | |
| α-helix | 257-260 | 4 | |
| α-helix | 266-275 | 10 | |
| α-helix | 286-290 | 5 | |
| α-helix | 293-296 | 4 | |
| α-helix | 300-303 | 4 | |
| α-helix | 304-306 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| CDK-activating kinase assembly factor MAT1 | H | protein | 328 | Homo sapiens | P51948 (AlphaFold model) |
| Cyclin-H | I | protein | 324 | Homo sapiens | P51946 (AlphaFold model) |
| Cyclin-dependent kinase 7 | J | protein | 391 | Homo sapiens | P50613 (AlphaFold model) |
| Cyclin-dependent kinase 1 | A | protein | 302 | Homo sapiens | P06493 (AlphaFold model) |
| G2/mitotic-specific cyclin-B1 | B | protein | 438 | Homo sapiens | P14635 |
Sequence of entity 1 (H), FASTA
>9SKQ_1 CDK-activating kinase assembly factor MAT1 (chains H)
MGSSHHHHHHENLYFQSNAMDDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR
GAGNCPECGTPLRKSNFRVQLFEDPTVDKEVEIRKKVLKIYNKREEDFPSLREYNDFLEE
VEEIVFNLTNNVDLDNTKKKMEIYQKENKDVIQKNKLKLTREQEELEEALEVERQENEQR
RLFIQKEEQLQQILKRKNKQAFLDELESSDLPVALLLAQHKDRSTQLEMQLEKPKPVKPV
TFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQ
DLAGGYTSSLACHRALQDAFSGLFWQPS
Sequence of entity 2 (I), FASTA
>9SKQ_2 Cyclin-H (chains I)
XMYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKY
YEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFN
VSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP
ILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLK
ENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYED
DDYVSKKSKHEEEEWTDDDLVESL
Sequence of entity 3 (J), FASTA
>9SKQ_3 Cyclin-dependent kinase 7 (chains J)
MASWSHPQFEKGGGSGGGSGGGSWSHPQFEKSGGGSENLYFQSNAMALDVKSRAKRYEKL
DFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNII
GLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILH
RDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVD
MWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGI
PLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVE
TLKEQSNPALAIKRKRTEALEQGGLPKKLIF
Sequence of entity 4 (A), FASTA
>9SKQ_4 Cyclin-dependent kinase 1 (chains A)
GPMGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLL
KELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQG
IVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVL
LGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQ
DYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIK
KM
Sequence of entity 5 (B), FASTA
>9SKQ_5 G2/mitotic-specific cyclin-B1 (chains B)
GAMGSMALRVTRNSKINAENKAKINMAGAKRVPTAPAATSKPGLRPRTALGDIGNKVSEQ
LQAKMPMKKEAKPSATGKVIDKKLPKPLEKVPMLVPVPVSEPVPEPEPEPEPEPVKEEKL
SPEPILVDTASPSPMETSGCAPAEEDLCQAFSDVILAVNDVDAEDGADPNLCSEYVKDIY
AYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQ
NNCVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKHQIRQMEMKILRALNF
GLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFPPSQIAAGAFCLALKI
LDNGEWTPTLQHYLSYTEESLLPVMQHLAKNVVMVNQGLTKHMTVKNKYATSKHAKISTL
PQLNSALVQDLAKAVAKV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1 |
| ANP | Phosphoaminophosphonic acid-adenylate ester | C10 H17 N6 O12 P3 | 2 |
Primary citation
Structural basis of T-loop-independent recognition and activation of CDKs by the CDK-activating kinase. Cushing, V.I., McGeoch, A.J.S., Williams, S.L. et al. Science (2025) 390:911-917. DOI 10.1126/science.adw0053 · PubMed
Other PDB entries of the same protein (UniProt P51948 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8P79 1.7 Å, Cryo-EM structure of CAK with averaged inhibitor density
- 8P77 1.8 Å, Cryo-EM structure of CAK in complex with inhibitor ICEC0943
- 8ORM 1.9 Å, Cryo-EM structure of CAK-THZ1
- 8P6V 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor ICEC0942
- 8P6W 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor BS-181
- 8P6X 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor BS-194
- 8P6Y 1.9 Å, Cryo-EM structure of CAK in complex with nucleotide analogue ATPgS
- 8P72 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor ICEC0768
- 8P78 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor dinaciclib
- 8PLZ 1.9 Å, Cryo-EM structure of CAK in complex with inhibitor CT7030
- 8P70 2.0 Å, Cryo-EM structure of CAK in complex with inhibitor ICEC0510-S
- 8P71 2.0 Å, Cryo-EM structure of CAK in complex with inhibitor ICEC0574
Browse structure collections
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