8S0T: CAK

Name: PDB 8S0T: Cryo-EM structure of CAK in complex with SY-5609
Published: 2024-12-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Cryo-EM structure of CAK in complex with SY-5609. Determined by electron microscopy at 2.3 Å resolution. Released 25 Dec 2024.

Method: Electron microscopy
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,261
Mol. weight: 87.81 kDa
Ligands: YNK
Released: 25 Dec 2024

Explore 8S0T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S0T contains 41 α-helices and 13 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: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	259-261	3
α-helix	265-269	5
α-helix	271-274	4
α-helix	276-279	4
α-helix	280-284	5
α-helix	289-301	13

Chain I: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	2-4	3
α-helix	6-11	6
α-helix	16-35	20
α-helix	50-70	21
α-helix	77-90	14
α-helix	101-115	15
α-helix	122-126	5
α-helix	133-153	21
α-helix	164-177	14
α-helix	184-187	4
α-helix	188-200	13
α-helix	202-205	4
α-helix	209-223	15
α-helix	229-230	2
α-helix	231-235	5
α-helix	242-261	20
α-helix	264-266	3
α-helix	267-282	16

Chain J: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-20	9	1
β-strand	24-31	8	1
β-strand	32	1	2
β-strand	34	1	2
β-strand	37-43	7	1
α-helix	57-66	10
β-strand	74	1	3
α-helix	75-76	2
β-strand	77-83	7	1
β-strand	86-92	7	1
β-strand	96-97	2	3
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	3
β-strand	151-153	3	3
β-strand	160-161	2	4
α-helix	176-178	3
α-helix	181-184	4
α-helix	193-208	16
α-helix	218-229	12
α-helix	240-242	3
α-helix	248-250	3
α-helix	257-260	4
α-helix	266-275	10
α-helix	284-285	2
α-helix	286-290	5
α-helix	293-296	4
α-helix	304-306	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
CDK-activating kinase assembly factor MAT1	H	protein	93	Homo sapiens	P51948 (AlphaFold model)
Cyclin-H	I	protein	324	Homo sapiens	P51946 (AlphaFold model)
Cyclin-dependent kinase 7	J	protein	349	Homo sapiens	P50613 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8S0T_1 CDK-activating kinase assembly factor MAT1 (chains H)
SNAPVTFSTGIKMGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVR
AASPQDLAGGYTSSLACHRALQDAFSGLFWQPS

Sequence of entity 2 (I), FASTA

>8S0T_2 Cyclin-H (chains I)
XMYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKY
YEKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFN
VSSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYP
ILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLK
ENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYED
DDYVSKKSKHEEEEWTDDDLVESL

Sequence of entity 3 (J), FASTA

>8S0T_3 Cyclin-dependent kinase 7 (chains J)
SNAMALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINR
TALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAY
MLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRW
YRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQW
PDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSN
RPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

Ligands and cofactors

ID	Name	Formula	Copies
YNK	7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(triflu…	C23 H26 F3 N6 O P	1

Primary citation

TFIIH kinase CDK7 drives cell proliferation through a common core transcription factor network. Jones, T., Feng, J., Luyties, O. et al. Sci Adv (2025) 11:eadr9660-eadr9660. DOI 10.1126/sciadv.adr9660 · 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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