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Open data
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Basic information
Entry | Database: PDB / ID: 8p6w | ||||||
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Title | Cryo-EM structure of CAK in complex with inhibitor BS-181 | ||||||
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Function / homology | ![]() negative regulation of DNA helicase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cushing, V.I. / Koh, A.F. / Feng, J. / Jurgaityte, K. / Bahl, A.K. / Ali, S. / Kotecha, A. / Greber, B.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design. Authors: Victoria I Cushing / Adrian F Koh / Junjie Feng / Kaste Jurgaityte / Alexander Bondke / Sebastian H B Kroll / Marion Barbazanges / Bodo Scheiper / Ash K Bahl / Anthony G M Barrett / Simak ...Authors: Victoria I Cushing / Adrian F Koh / Junjie Feng / Kaste Jurgaityte / Alexander Bondke / Sebastian H B Kroll / Marion Barbazanges / Bodo Scheiper / Ash K Bahl / Anthony G M Barrett / Simak Ali / Abhay Kotecha / Basil J Greber / ![]() ![]() ![]() ![]() Abstract: Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to ...Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.5 KB | Display | ![]() |
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PDB format | ![]() | 105.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 17509MC ![]() 8ormC ![]() 8p6vC ![]() 8p6xC ![]() 8p6yC ![]() 8p6zC ![]() 8p70C ![]() 8p71C ![]() 8p72C ![]() 8p73C ![]() 8p74C ![]() 8p75C ![]() 8p76C ![]() 8p77C ![]() 8p78C ![]() 8p79C ![]() 8p7lC ![]() 8plzC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 10234.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 37721.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | ![]() Mass: 39362.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P50613, ![]() |
#4: Chemical | ChemComp-X2H / ~{ Mass: 380.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H32N6 / Feature type: SUBJECT OF INVESTIGATION |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: CDK-activating kinase![]() | |||||||||||||||||||||||||
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Molecular weight | Value: 0.085 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.9 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5203 |
EM imaging optics | Energyfilter name![]() |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 565148 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8ORM Accession code: 8ORM / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||
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