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- EMDB-11823: Cryo-EM structure of the human CAK bound to ICEC0942 at 2.6 Angst... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11823 | |||||||||
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Title | Cryo-EM structure of the human CAK bound to ICEC0942 at 2.6 Angstroms resolution | |||||||||
![]() | Post-processed (sharpened, filtered) cryo-EM map | |||||||||
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Function / homology | ![]() negative regulation of DNA helicase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Greber BJ / Remis J / Ali S / Nogales E | |||||||||
Funding support | ![]()
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![]() | ![]() Title: 2.5 Å-resolution structure of human CDK-activating kinase bound to the clinical inhibitor ICEC0942. Authors: Basil J Greber / Jonathan Remis / Simak Ali / Eva Nogales / ![]() ![]() Abstract: The human CDK-activating kinase (CAK), composed of CDK7, cyclin H, and MAT1, is involved in the control of transcription initiation and the cell cycle. Because of these activities, it has been ...The human CDK-activating kinase (CAK), composed of CDK7, cyclin H, and MAT1, is involved in the control of transcription initiation and the cell cycle. Because of these activities, it has been identified as a promising target for cancer chemotherapy. A number of CDK7 inhibitors have entered clinical trials, among them ICEC0942 (also known as CT7001). Structural information can aid in improving the affinity and specificity of such drugs or drug candidates, reducing side effects in patients. Here, we have determined the structure of the human CAK in complex with ICEC0942 at 2.5 Å-resolution using cryogenic electron microscopy. Our structure reveals conformational differences of ICEC0942 compared with previous X-ray crystal structures of the CDK2-bound complex, and highlights the critical ability of cryogenic electron microscopy to resolve structures of drug-bound protein complexes without the need to crystalize the protein target. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.6 KB 18.6 KB | Display Display | ![]() |
Images | ![]() | 56.5 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() | 49.6 MB 49.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b5oC ![]() 7b5qC C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 3.8 TB Data #1: Unaligned movies of human CAK-ICEC0942, dataset 1 [micrographs - multiframe] Data #2: Unaligned movies of human CAK-ICEC0942, dataset 3 [micrographs - multiframe] Data #3: Unaligned movies of human CAK-ICEC0942, dataset 2 [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Post-processed (sharpened, filtered) cryo-EM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.029 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map
File | emd_11823_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map
File | emd_11823_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : CDK-activating kinase
Entire | Name: CDK-activating kinase![]() |
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Components |
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-Supramolecule #1: CDK-activating kinase
Supramolecule | Name: CDK-activating kinase / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 120 KDa |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.9 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | Incubated with 50 uM inhibitor for 5 min |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 72886 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | Automated procedure in SerialEM |
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 3571 / #0 - Average exposure time: 2.0 sec. / #0 - Average electron dose: 69.0 e/Å2 #0 - Details: Movies (69 frames) acquired in 3 x 3 pattern by image shift #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number grids imaged: 2 / #1 - Number real images: 5302 / #1 - Average exposure time: 2.0 sec. / #1 - Average electron dose: 69.0 e/Å2 #1 - Details: Movies (69 frames) acquired in 3 x 3 pattern by image shift |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 10904715 | ||||||
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CTF correction | Software:
Details: Implemented in RELION 3.1 | ||||||
Startup model | Type of model: EMDB MAP EMDB ID: | ||||||
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) | ||||||
Final 3D classification | Number classes: 6 / Avg.num./class: 33300 / Software - Name: RELION (ver. 3.1) Details: High-resolution, masked, classification using 6 classes and a tau value of 72. | ||||||
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) | ||||||
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 20379 | ||||||
Image recording ID | 1 |