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8p6x

Cryo-EM structure of CAK in complex with inhibitor BS-194

Method: ELECTRON MICROSCOPY Dmax: 89.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CDK-activating kinase assembly factor MAT1

Homo sapiens

UniProt P51948

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain H； UniProt 220–309 Not recorded Cyclin-H × 1 （P51946） Cyclin-dependent kinase 7 × 1 （P50613） NS9 (2S,3S)-3-{[7-(benzylamino)-3-(1-methylethyl)pyrazolo[1,5-a]pyrimidin-5-yl]amino}butane-1,2,4-triol × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 1.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8P6X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1G25 SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE HUMAN TFIIH MAT1 SUBUNIT Deposited 2000-10-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–65（65 aa） Fragment：N-TERMINAL DOMAIN
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Pressure ambiant
NMR measurement conditions pH 7.5；290 K；Pressure ambiant
NMR measurement conditions pH 7.5；283 K；Pressure ambiant
NMR sample composition 2 mM MAT1; 20 mM Tris-HCl pH 7.5; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
28JM Cryo-EM structure of the human holo-TFIIH and XPC initial encounter complex Deposited 2026-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.29 Å
28JS Cryo-EM structure of the human holo-TFIIH-XPC complex bound to bulky lesion-mimic DNA (composite map) Deposited 2026-02-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain H 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.32 Å
28JV Cryo-EM structure of the human holo-TFIIH-XPC complex bound to bulky lesion-mimic DNA (consensus map) Deposited 2026-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain H 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.91 Å
28KE Cryo-EM structure of the human holo-TFIIH-XPC-XPA complex bound to bulky lesion-mimic DNA Deposited 2026-02-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain H 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM GP2
Resolution 3.60 Å
6NMI Cryo-EM structure of the human TFIIH core complex Deposited 2019-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；A thin film of continuous carbon was floated onto Protochips C-flat CF-4/2 holey carbon grids and glow discharged or plasma cleaned before application of 4 uL of sample solution.
Resolution 3.70 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain 3 1–309（309 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6O9M Structure of the human apo TFIIH Deposited 2019-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain 3 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6TUN Helicase domain complex Deposited 2020-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 66–141（76 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris pH 8.5 25% PEG8000
Resolution 2.07 Å R-free 0.227
6TUN Helicase domain complex Deposited 2020-01-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 66–141（76 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；100 mM Tris pH 8.5 25% PEG8000
Resolution 2.07 Å R-free 0.227
6XBZ Structure of the human CDK-activating kinase Deposited 2020-06-07 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–309（309 aa）
Not recorded MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6XD3 Structure of the human CAK in complex with THZ1 Deposited 2020-06-09 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa） Fragment：residues 220-309
Not recorded V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7B5O Cryo-EM structure of the human CAK bound to ICEC0942 at 2.5 Angstroms resolution Deposited 2020-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–309（309 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.50 Å
7B5Q Cryo-EM structure of the human CAK bound to ICEC0942 (PHENIX-OPLS3e) Deposited 2020-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–309（309 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.50 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain d 1–309（309 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain 3 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
7NVW TFIIH in a pre-translocated state (without ADP-BeF3) Deposited 2021-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain 3 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7NVX TFIIH in a post-translocated state (with ADP-BeF3) Deposited 2021-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain 3 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 3 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 3 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 3 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain 7 1–309（309 aa）
Mutation：0 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain 7 1–309（309 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain HD 1–309（309 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain HD 1–309（309 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8ORM Cryo-EM structure of CAK-THZ1 Deposited 2023-04-14 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6V Cryo-EM structure of CAK in complex with inhibitor ICEC0942 Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6W Cryo-EM structure of CAK in complex with inhibitor BS-181 Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded X2H ~{N}5-(6-azanylhexyl)-~{N}7-(phenylmethyl)-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6Y Cryo-EM structure of CAK in complex with nucleotide analogue ATPgS Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6Z Cryo-EM structure of CAK in complex with inhibitor ICEC0510-R Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded X4L N7-(phenylmethyl)-3-propan-2-yl-N5-[(3R)-pyrrolidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
8P70 Cryo-EM structure of CAK in complex with inhibitor ICEC0510-S Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded X4Q N7-(phenylmethyl)-3-propan-2-yl-N5-[(3S)-pyrrolidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P71 Cryo-EM structure of CAK in complex with inhibitor ICEC0574 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded X4F (3R,4S)-4-[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]pyrrolidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P72 Cryo-EM structure of CAK in complex with inhibitor ICEC0768 Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded X2Z ~{N}7-(phenylmethyl)-~{N}5-[(3~{S})-piperidin-3-yl]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P73 Cryo-EM structure of CAK in complex with inhibitor ICEC0829 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded X50 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidine-3,4-diol × 1 X58 (3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidine-3,4-diol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P74 Cryo-EM structure of CAK in complex with inhibitor ICEC0880 (ring-up conformation) Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded X3Z (2S,3S)-3-[[7-[(2-bromophenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]butane-1,2,4-triol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8P75 Cryo-EM structure of CAK in complex with inhibitor ICEC0880 (ring-down conformation) Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded X3Z (2S,3S)-3-[[7-[(2-bromophenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]butane-1,2,4-triol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P76 Cryo-EM structure of CAK in complex with inhibitor ICEC0914 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded X1W N5-[(3S,4R)-4-phenylmethoxypyrrolidin-3-yl]-N7-(phenylmethyl)-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P77 Cryo-EM structure of CAK in complex with inhibitor ICEC0943 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded I73 (3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.80 Å
8P78 Cryo-EM structure of CAK in complex with inhibitor dinaciclib Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded 1QK 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P79 Cryo-EM structure of CAK with averaged inhibitor density Deposited 2023-05-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Structure obtained by combining data from six samples of CAK bound to different non-covalent inhibitors. Four samples contained 5 mM beta-mercaptoethanol and two samples did not.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.70 Å
8P7L Cryo-EM structure of CDK7 subunit of CAK in complex with inhibitor LDC4297 Deposited 2023-05-30 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–309（309 aa）
Not recorded WD9 2-[(3S)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
8PLZ Cryo-EM structure of CAK in complex with inhibitor CT7030 Deposited 2023-06-27 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded ZQ6 (3~{R},4~{R})-4-[[[7-[(2-methoxyphenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8PYR Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex Deposited 2023-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 230–309（80 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1 M Hepes (pH 7.0), 12% (v/w) medium weight PEG mix of PEG6K and PEG4K, 10% ethylene-glycol, and 0.2 M NDSB
Resolution 2.15 Å R-free 0.241
8PYR Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex Deposited 2023-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 230–309（80 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1 M Hepes (pH 7.0), 12% (v/w) medium weight PEG mix of PEG6K and PEG4K, 10% ethylene-glycol, and 0.2 M NDSB
Resolution 2.15 Å R-free 0.241
8S0R Cryo-EM structure of CAK modified by covalent inhibitor SY-1365 Deposited 2024-02-14 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded A1H46 ~{N}-[(1~{S},3~{R})-3-[[5-chloranyl-4-(1~{H}-indol-3-yl)pyrimidin-2-yl]amino]-1-methyl-cyclohexyl]-5-[4-(dimethylamino)butanoylamino]pyridine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8S0T Cryo-EM structure of CAK in complex with SY-5609 Deposited 2024-02-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded YNK 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer contained 54 uM inhibitor SY-5609.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric
Chain 0 1–309（309 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.13 Å
9HIX Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with THZ1 Deposited 2024-11-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9HIY Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with ATPgS Deposited 2024-11-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9HJ0 Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with Samuraciclib Deposited 2024-11-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9I9I Cryo-EM structure of CAK-CDK11 Deposited 2025-02-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 1–309（309 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9I9J Cryo-EM structure of CAK-CDK2 (determined in the presence of ADP-nitrate) Deposited 2025-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 1–309（309 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9I9K Cryo-EM structure of CAK-CDK2 (determined in the presence of ADP-AlFx) Deposited 2025-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 1–309（309 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9QCV Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP Deposited 2025-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–309（309 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9QCX Cryo-EM structure of apo-CAK-CDK2-cyclin A2 Deposited 2025-03-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–309（309 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9QJN Cryo-EM structure of the human CAK bound to OTS964 Deposited 2025-03-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 220–309（90 aa）
Not recorded NK3 OTS964 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9SKQ Cryo-EM structure of CAK-CDK1-cyclin B1 Deposited 2025-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–309（309 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

66 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MAT1_HUMAN
Isoform P51948-1
PDB entities 1
Chains and sequence ranges Author chain H； PDBConstruct 4–93； UniProt 220–309

Cyclin-H

Homo sapiens

UniProt P51946

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain I； UniProt 1–323 Non-standard monomer：Yes (specific site not provided by mmCIF) CDK-activating kinase assembly factor MAT1 × 1 （P51948） Cyclin-dependent kinase 7 × 1 （P50613） NS9 (2S,3S)-3-{[7-(benzylamino)-3-(1-methylethyl)pyrazolo[1,5-a]pyrimidin-5-yl]amino}butane-1,2,4-triol × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 1.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8P6X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JKW STRUCTURE OF CYCLIN MCS2 Deposited 1996-10-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–323（323 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å R-free 0.272
1KXU CYCLIN H, A POSITIVE REGULATORY SUBUNIT OF CDK ACTIVATING KINASE Deposited 1996-08-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–323（323 aa）
Mutation：INS(MSHHHHHHGS-M1) (HISTIDINE TAG) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å R-free 0.295
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain 9 1–323（323 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XBZ Structure of the human CDK-activating kinase Deposited 2020-06-07 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Not recorded MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6XD3 Structure of the human CAK in complex with THZ1 Deposited 2020-06-09 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Not recorded V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7B5O Cryo-EM structure of the human CAK bound to ICEC0942 at 2.5 Angstroms resolution Deposited 2020-12-05 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.50 Å
7B5Q Cryo-EM structure of the human CAK bound to ICEC0942 (PHENIX-OPLS3e) Deposited 2020-12-05 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.50 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain 9 1–323（323 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain 9 1–323（323 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain 9 1–323（323 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain 9 1–323（323 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain f 1–323（323 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain 9 1–323（323 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain 9 1–323（323 aa）
Mutation：0 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain 9 1–323（323 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain HJ 1–323（323 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain HJ 1–323（323 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8ORM Cryo-EM structure of CAK-THZ1 Deposited 2023-04-14 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6V Cryo-EM structure of CAK in complex with inhibitor ICEC0942 Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6W Cryo-EM structure of CAK in complex with inhibitor BS-181 Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) X2H ~{N}5-(6-azanylhexyl)-~{N}7-(phenylmethyl)-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6Y Cryo-EM structure of CAK in complex with nucleotide analogue ATPgS Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6Z Cryo-EM structure of CAK in complex with inhibitor ICEC0510-R Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) X4L N7-(phenylmethyl)-3-propan-2-yl-N5-[(3R)-pyrrolidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
8P70 Cryo-EM structure of CAK in complex with inhibitor ICEC0510-S Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) X4Q N7-(phenylmethyl)-3-propan-2-yl-N5-[(3S)-pyrrolidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P71 Cryo-EM structure of CAK in complex with inhibitor ICEC0574 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) X4F (3R,4S)-4-[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]pyrrolidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P72 Cryo-EM structure of CAK in complex with inhibitor ICEC0768 Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) X2Z ~{N}7-(phenylmethyl)-~{N}5-[(3~{S})-piperidin-3-yl]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P73 Cryo-EM structure of CAK in complex with inhibitor ICEC0829 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) X50 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidine-3,4-diol × 1 X58 (3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidine-3,4-diol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P74 Cryo-EM structure of CAK in complex with inhibitor ICEC0880 (ring-up conformation) Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) X3Z (2S,3S)-3-[[7-[(2-bromophenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]butane-1,2,4-triol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8P75 Cryo-EM structure of CAK in complex with inhibitor ICEC0880 (ring-down conformation) Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) X3Z (2S,3S)-3-[[7-[(2-bromophenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]butane-1,2,4-triol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P76 Cryo-EM structure of CAK in complex with inhibitor ICEC0914 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) X1W N5-[(3S,4R)-4-phenylmethoxypyrrolidin-3-yl]-N7-(phenylmethyl)-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P77 Cryo-EM structure of CAK in complex with inhibitor ICEC0943 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) I73 (3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.80 Å
8P78 Cryo-EM structure of CAK in complex with inhibitor dinaciclib Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 1QK 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P79 Cryo-EM structure of CAK with averaged inhibitor density Deposited 2023-05-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Structure obtained by combining data from six samples of CAK bound to different non-covalent inhibitors. Four samples contained 5 mM beta-mercaptoethanol and two samples did not.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.70 Å
8PLZ Cryo-EM structure of CAK in complex with inhibitor CT7030 Deposited 2023-06-27 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZQ6 (3~{R},4~{R})-4-[[[7-[(2-methoxyphenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8PYR Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex Deposited 2023-07-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–323（323 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1 M Hepes (pH 7.0), 12% (v/w) medium weight PEG mix of PEG6K and PEG4K, 10% ethylene-glycol, and 0.2 M NDSB
Resolution 2.15 Å R-free 0.241
8PYR Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex Deposited 2023-07-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–323（323 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1 M Hepes (pH 7.0), 12% (v/w) medium weight PEG mix of PEG6K and PEG4K, 10% ethylene-glycol, and 0.2 M NDSB
Resolution 2.15 Å R-free 0.241
8S0R Cryo-EM structure of CAK modified by covalent inhibitor SY-1365 Deposited 2024-02-14 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) A1H46 ~{N}-[(1~{S},3~{R})-3-[[5-chloranyl-4-(1~{H}-indol-3-yl)pyrimidin-2-yl]amino]-1-methyl-cyclohexyl]-5-[4-(dimethylamino)butanoylamino]pyridine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8S0T Cryo-EM structure of CAK in complex with SY-5609 Deposited 2024-02-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) YNK 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer contained 54 uM inhibitor SY-5609.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9HIX Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with THZ1 Deposited 2024-11-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9HIY Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with ATPgS Deposited 2024-11-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9HJ0 Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with Samuraciclib Deposited 2024-11-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9I9I Cryo-EM structure of CAK-CDK11 Deposited 2025-02-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9I9J Cryo-EM structure of CAK-CDK2 (determined in the presence of ADP-nitrate) Deposited 2025-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9I9K Cryo-EM structure of CAK-CDK2 (determined in the presence of ADP-AlFx) Deposited 2025-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9QCV Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP Deposited 2025-03-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9QCX Cryo-EM structure of apo-CAK-CDK2-cyclin A2 Deposited 2025-03-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9QJN Cryo-EM structure of the human CAK bound to OTS964 Deposited 2025-03-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NK3 OTS964 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9SKQ Cryo-EM structure of CAK-CDK1-cyclin B1 Deposited 2025-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 1–323（323 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

46 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCNH_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain I； PDBConstruct 2–324； UniProt 1–323

Cyclin-dependent kinase 7

Homo sapiens

UniProt P50613

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain J； UniProt 1–346 Not recorded CDK-activating kinase assembly factor MAT1 × 1 （P51948） Cyclin-H × 1 （P51946） NS9 (2S,3S)-3-{[7-(benzylamino)-3-(1-methylethyl)pyrazolo[1,5-a]pyrimidin-5-yl]amino}butane-1,2,4-triol × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 1.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8P6X Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1UA2 Crystal Structure of Human CDK7 Deposited 2004-08-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–346（346 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
Resolution 3.02 Å R-free 0.288
1UA2 Crystal Structure of Human CDK7 Deposited 2004-08-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–346（346 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
Resolution 3.02 Å R-free 0.288
1UA2 Crystal Structure of Human CDK7 Deposited 2004-08-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–346（346 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
Resolution 3.02 Å R-free 0.288
1UA2 Crystal Structure of Human CDK7 Deposited 2004-08-11 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–346（346 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
Resolution 3.02 Å R-free 0.288
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain 8 1–346（346 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XBZ Structure of the human CDK-activating kinase Deposited 2020-06-07 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6XD3 Structure of the human CAK in complex with THZ1 Deposited 2020-06-09 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7B5O Cryo-EM structure of the human CAK bound to ICEC0942 at 2.5 Angstroms resolution Deposited 2020-12-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.50 Å
7B5Q Cryo-EM structure of the human CAK bound to ICEC0942 (PHENIX-OPLS3e) Deposited 2020-12-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.50 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain 8 1–346（346 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain 8 1–346（346 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain 8 1–346（346 aa）
Not recorded ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric
Chain 8 1–346（346 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain e 1–346（346 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain 8 1–346（346 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric
Chain 8 1–346（346 aa）
Mutation：0 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric
Chain 8 1–346（346 aa）
Not recorded SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain HI 1–346（346 aa）
Mutation：K41A ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric
Chain HI 1–346（346 aa）
Mutation：K41A ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.16 Å
8ORM Cryo-EM structure of CAK-THZ1 Deposited 2023-04-14 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P4Z Crystal structure of the human CDK7 kinase domain in complex with LDC4297 Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 10–311（302 aa）
Not recorded WZ8 2-[(3R)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine × 1 GOL GLYCEROL × 2 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M ammonium acetate, 0.1 M sodium citrate, 12% w/v PEG 3350, 0.2 M NDSB-201
Resolution 2.75 Å R-free 0.251
8P4Z Crystal structure of the human CDK7 kinase domain in complex with LDC4297 Deposited 2023-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 10–311（302 aa）
Not recorded WZ8 2-[(3R)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine × 1 GOL GLYCEROL × 6 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M ammonium acetate, 0.1 M sodium citrate, 12% w/v PEG 3350, 0.2 M NDSB-201
Resolution 2.75 Å R-free 0.251
8P6V Cryo-EM structure of CAK in complex with inhibitor ICEC0942 Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6W Cryo-EM structure of CAK in complex with inhibitor BS-181 Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded X2H ~{N}5-(6-azanylhexyl)-~{N}7-(phenylmethyl)-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6Y Cryo-EM structure of CAK in complex with nucleotide analogue ATPgS Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P6Z Cryo-EM structure of CAK in complex with inhibitor ICEC0510-R Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded X4L N7-(phenylmethyl)-3-propan-2-yl-N5-[(3R)-pyrrolidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
8P70 Cryo-EM structure of CAK in complex with inhibitor ICEC0510-S Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded X4Q N7-(phenylmethyl)-3-propan-2-yl-N5-[(3S)-pyrrolidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P71 Cryo-EM structure of CAK in complex with inhibitor ICEC0574 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded X4F (3R,4S)-4-[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]pyrrolidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P72 Cryo-EM structure of CAK in complex with inhibitor ICEC0768 Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded X2Z ~{N}7-(phenylmethyl)-~{N}5-[(3~{S})-piperidin-3-yl]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P73 Cryo-EM structure of CAK in complex with inhibitor ICEC0829 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded X50 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidine-3,4-diol × 1 X58 (3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidine-3,4-diol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P74 Cryo-EM structure of CAK in complex with inhibitor ICEC0880 (ring-up conformation) Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded X3Z (2S,3S)-3-[[7-[(2-bromophenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]butane-1,2,4-triol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8P75 Cryo-EM structure of CAK in complex with inhibitor ICEC0880 (ring-down conformation) Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded X3Z (2S,3S)-3-[[7-[(2-bromophenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]butane-1,2,4-triol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P76 Cryo-EM structure of CAK in complex with inhibitor ICEC0914 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded X1W N5-[(3S,4R)-4-phenylmethoxypyrrolidin-3-yl]-N7-(phenylmethyl)-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8P77 Cryo-EM structure of CAK in complex with inhibitor ICEC0943 Deposited 2023-05-30 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded I73 (3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.80 Å
8P78 Cryo-EM structure of CAK in complex with inhibitor dinaciclib Deposited 2023-05-30 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded 1QK 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8P79 Cryo-EM structure of CAK with averaged inhibitor density Deposited 2023-05-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Structure obtained by combining data from six samples of CAK bound to different non-covalent inhibitors. Four samples contained 5 mM beta-mercaptoethanol and two samples did not.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.70 Å
8P7L Cryo-EM structure of CDK7 subunit of CAK in complex with inhibitor LDC4297 Deposited 2023-05-30 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 1–346（346 aa）
Not recorded WD9 2-[(3S)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.10 Å
8PLZ Cryo-EM structure of CAK in complex with inhibitor CT7030 Deposited 2023-06-27 Different ligand/ion Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded ZQ6 (3~{R},4~{R})-4-[[[7-[(2-methoxyphenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8PYR Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex Deposited 2023-07-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–346（346 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1 M Hepes (pH 7.0), 12% (v/w) medium weight PEG mix of PEG6K and PEG4K, 10% ethylene-glycol, and 0.2 M NDSB
Resolution 2.15 Å R-free 0.241
8PYR Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex Deposited 2023-07-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–346（346 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1 M Hepes (pH 7.0), 12% (v/w) medium weight PEG mix of PEG6K and PEG4K, 10% ethylene-glycol, and 0.2 M NDSB
Resolution 2.15 Å R-free 0.241
8R99 A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–346（346 aa）
Mutation：W132R, S164D, T170E ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；.1M (NH4)3 citrate .2M NDSB-201 15.2% PEG 3350
Resolution 1.81 Å R-free 0.220
8R9A A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–346（346 aa）
Mutation：W132R,S164D, T170E PEG DI(HYDROXYETHYL)ETHER × 1 I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；.2M Na2HPO4 20% PEG 3350
Resolution 1.71 Å R-free 0.294
8R9B A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–326（326 aa）
Mutation：S164D, T170E, del327-346 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；19% 2-propanol, 5% glycerol, 19%PEG4K, 0.095M Na3citrate pH5.6/HCl
Resolution 2.21 Å R-free 0.243
8R9B A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–326（326 aa）
Mutation：S164D, T170E, del327-346 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；19% 2-propanol, 5% glycerol, 19%PEG4K, 0.095M Na3citrate pH5.6/HCl
Resolution 2.21 Å R-free 0.243
8R9B A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–326（326 aa）
Mutation：S164D, T170E, del327-346 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；19% 2-propanol, 5% glycerol, 19%PEG4K, 0.095M Na3citrate pH5.6/HCl
Resolution 2.21 Å R-free 0.243
8R9B A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–326（326 aa）
Mutation：S164D, T170E, del327-346 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；19% 2-propanol, 5% glycerol, 19%PEG4K, 0.095M Na3citrate pH5.6/HCl
Resolution 2.21 Å R-free 0.243
8R9O A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–346（346 aa）
Mutation：W132R,S164D, T170E YN3 ~{N}-[(1~{S})-2-(dimethylamino)-1-phenyl-ethyl]-6,6-dimethyl-3-[[4-(propanoylamino)phenyl]carbonylamino]-1,4-dihydropyrrolo[3,4-c]pyrazole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M (NH4)3 citrate 15% PEG 3350
Resolution 2.22 Å R-free 0.344
8R9O A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–346（346 aa）
Mutation：W132R,S164D, T170E YN3 ~{N}-[(1~{S})-2-(dimethylamino)-1-phenyl-ethyl]-6,6-dimethyl-3-[[4-(propanoylamino)phenyl]carbonylamino]-1,4-dihydropyrrolo[3,4-c]pyrazole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M (NH4)3 citrate 15% PEG 3350
Resolution 2.22 Å R-free 0.344
8R9S A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–346（346 aa）
Mutation：W132R,S164D, T170E PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 YPK [(3S)-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% Glycerol .02M KNa tartrate .02M NH4 acetate .02M Na formate .02M Na oxamate .02M Na3 citrate 10% PEG 4000 .1M pH=7.5 MOPS/NaHEPES
Resolution 2.78 Å R-free 0.296
8R9S A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–346（346 aa）
Mutation：W132R,S164D, T170E PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 2 YPK [(3S)-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% Glycerol .02M KNa tartrate .02M NH4 acetate .02M Na formate .02M Na oxamate .02M Na3 citrate 10% PEG 4000 .1M pH=7.5 MOPS/NaHEPES
Resolution 2.78 Å R-free 0.296
8R9U A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–346（346 aa）
Mutation：W132R,S164D, T170E YNK 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M (NH4)3 citrate 15% PEG 3350
Resolution 1.94 Å R-free 0.340
8R9U A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–346（346 aa）
Mutation：W132R,S164D, T170E YNK 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M (NH4)3 citrate 15% PEG 3350
Resolution 1.94 Å R-free 0.340
8S0R Cryo-EM structure of CAK modified by covalent inhibitor SY-1365 Deposited 2024-02-14 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded A1H46 ~{N}-[(1~{S},3~{R})-3-[[5-chloranyl-4-(1~{H}-indol-3-yl)pyrimidin-2-yl]amino]-1-methyl-cyclohexyl]-5-[4-(dimethylamino)butanoylamino]pyridine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8S0T Cryo-EM structure of CAK in complex with SY-5609 Deposited 2024-02-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded YNK 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9；Buffer contained 54 uM inhibitor SY-5609.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9HIX Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with THZ1 Deposited 2024-11-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9HIY Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with ATPgS Deposited 2024-11-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
9HJ0 Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with Samuraciclib Deposited 2024-11-27 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9I9I Cryo-EM structure of CAK-CDK11 Deposited 2025-02-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–346（346 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9I9J Cryo-EM structure of CAK-CDK2 (determined in the presence of ADP-nitrate) Deposited 2025-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–346（346 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9I9K Cryo-EM structure of CAK-CDK2 (determined in the presence of ADP-AlFx) Deposited 2025-02-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain J 1–346（346 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9QCV Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP Deposited 2025-03-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 1–346（346 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9QCX Cryo-EM structure of apo-CAK-CDK2-cyclin A2 Deposited 2025-03-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 1–346（346 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9QJN Cryo-EM structure of the human CAK bound to OTS964 Deposited 2025-03-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–346（346 aa）
Not recorded NK3 OTS964 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9SKQ Cryo-EM structure of CAK-CDK1-cyclin B1 Deposited 2025-09-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain J 1–346（346 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

53 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDK7_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain J； PDBConstruct 4–349； UniProt 1–346

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8p6x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8p6x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8p6x
Deposition date deposition_date2023-05-30
Structure title titleCryo-EM structure of CAK in complex with inhibitor BS-194
Keywords keywordsKinase, Inhibitor, Transcription, Cell Cycle, TRANSFERASE; TRANSFERASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.60 Å
Radius of gyration Rg (electron density) rg_electron26.65 Å
Forward intensity I(0) i080546100.00
Molecular weight molecular_weight72591.0 kDa
Excluded volume excluded_volume91845 ų
Envelope volume envelope_volume108270 ų
Hydration-shell volume shell_volume33522 ų
Envelope diameter envelope_diameter93.5 Å
Shell Rg shell_rg34.28 Å
Envelope Rg envelope_rg26.79 Å
Shape Rg shape_rg26.63 Å
Total Rg total_rg27.51 Å
Total atoms total_atoms5112
Residues n_residues631
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.0 Å
Rg (real space) rg_real27.52 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real8.0550e+07
I(0) uncertainty (real space) i0_real_error1.3270e+06
Rg (reciprocal space) rg_reciprocal27.55 Å
I(0) (reciprocal space) i0_reciprocal80550000.0000
Solution quality estimate total_estimate0.8977
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.8 Å
Skewness Skewness skewness0.275
Kurtosis Kurtosis kurtosis-0.416
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24980000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.964
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)