8PYR: Cyclin-dependent kinase 7

Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex. Determined by X-ray diffraction at 2.15 Å resolution. Released 6 Mar 2024.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Homo sapiens, Lama glama
Chains: 8
Atoms: 12,032
Mol. weight: 197.24 kDa
Released: 6 Mar 2024

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

Secondary structure: helices and β-sheets

8PYR contains 89 α-helices and 41 β-strands across 8 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: 16 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	57-66	10
β-strand	74	1	1
β-strand	77-83	7	2
β-strand	86-91	6	2
β-strand	96-97	2	1
α-helix	98-103	6
α-helix	111-130	20
β-strand	133-134	2	3
α-helix	140-142	3
β-strand	143-145	3	1
β-strand	151-153	3	1
β-strand	160-161	2	3
α-helix	176-178	3
α-helix	181-184	4
β-strand	190	1	4
α-helix	193-208	16
α-helix	218-229	12
α-helix	238-242	5
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	301-303	3
α-helix	304-306	3

Chain B: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	2-4	3
α-helix	6-10	5
α-helix	16-36	21
α-helix	48-49	2
α-helix	50-69	20
α-helix	74-76	3
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	188-198	11
α-helix	203-205	3
α-helix	209-223	15
α-helix	229-230	2
α-helix	231-235	5
α-helix	242-260	19
α-helix	264-266	3
α-helix	267-282	16

Chain C: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	258-262	5
α-helix	263-268	6
α-helix	271-274	4
α-helix	276-279	4
α-helix	280-285	6
β-strand	286	1	4
α-helix	289-301	13

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	10-12	3	6
β-strand	18-25	8	5
α-helix	29-31	3
β-strand	34-39	6	6
β-strand	45-51	7	6
β-strand	58-60	3	6
α-helix	62-64	3
β-strand	68-73	6	5
β-strand	78-83	6	5
α-helix	88-90	3
β-strand	92-98	7	6
β-strand	104-105	2	6
β-strand	109-113	5	6

Chain E: 15 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	57-66	10
β-strand	74	1	7
β-strand	77-83	7	8
β-strand	86-91	6	8
β-strand	96-97	2	7
α-helix	98-103	6
α-helix	111-130	20
β-strand	133-134	2	9
α-helix	140-142	3
β-strand	143-145	3	7
β-strand	151-153	3	7
β-strand	160-161	2	9
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	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	300-302	3

Chain F: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	2-4	3
α-helix	6-10	5
α-helix	16-36	21
α-helix	48-49	2
α-helix	50-69	20
α-helix	74-76	3
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	184-186	3
α-helix	187-198	12
α-helix	203-205	3
α-helix	209-223	15
α-helix	229-230	2
α-helix	231-235	5
α-helix	242-260	19
α-helix	264-266	3
α-helix	267-282	16

Chain G: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	258-262	5
α-helix	263-268	6
α-helix	271-274	4
α-helix	276-279	4
α-helix	280-284	5
α-helix	289-301	13

Chain H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	104-105	2	12
β-strand	109-111	3	12
β-strand	112-113	2	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 7	A, E	protein	346	Homo sapiens	P50613 (AlphaFold model)
Cyclin-H	B, F	protein	323	Homo sapiens	P51946 (AlphaFold model)
CDK-activating kinase assembly factor MAT1	C, G	protein	82	Homo sapiens	P51948 (AlphaFold model)
Nanobody (VHH-RD7-04)	D, H	protein	115	Lama glama

Sequence of entity 1 (A, E), FASTA

>8PYR_1 Cyclin-dependent kinase 7 (chains A, E)
MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTAL
REIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLM
TLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRA
PELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDM
CSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPG
PTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF

Sequence of entity 2 (B, F), FASTA

>8PYR_2 Cyclin-H (chains B, F)
MYHNSSQKRHWTFSSEEQLARLRADANRKFRCKAVANGKVLPNDPVFLEPHEEMTLCKYY
EKRLLEFCSVFKPAMPRSVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNV
SSPQFVGNLRESPLGQEKALEQILEYELLLIQQLNFHLIVHNPYRPFEGFLIDLKTRYPI
LENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLMLKE
NRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDD
DYVSKKSKHEEEEWTDDDLVESL

Sequence of entity 3 (C, G), FASTA

>8PYR_3 CDK-activating kinase assembly factor MAT1 (chains C, G)
GSGQHISLAPIHKLEEALYEYQPLQIETYGPHVPELEMLGRLGYLNHVRAASPQDLAGGY
TSSLACHRALQDAFSGLFWQPS

Sequence of entity 4 (D, H), FASTA

>8PYR_4 Nanobody (VHH-RD7-04) (chains D, H)
QVQLVESGGGLVQPGGSLRLSCVASGFTFKNFYMGWVRQAPDKGLEWVATINSGGEIQSY
ADSVKGRFTISRDNAKNTLYLQMNNLRPEDTAVYYCSKQSSTPAKGQGTQVTVSS

Primary citation

Structural basis of Cdk7 activation by dual T-loop phosphorylation. Duster, R., Anand, K., Binder, S.C. et al. Nat Commun (2024) 15:6597-6597. DOI 10.1038/s41467-024-50891-z · PubMed

Other PDB entries of the same protein (UniProt P50613 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P79 1.7 Å, Cryo-EM structure of CAK with averaged inhibitor density
8R9A 1.71 Å, A soakable crystal form of human CDK7 in complex with AMP-PNP
8P77 1.8 Å, Cryo-EM structure of CAK in complex with inhibitor ICEC0943
8R99 1.81 Å, A soakable crystal form of human CDK7 in complex with AMP-PNP
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

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