+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22123 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the human CDK-activating kinase | |||||||||||||||
Map data | Post-processed map, clipped to 150 pixel box size (as used for coordinate refinement) | |||||||||||||||
Sample |
| |||||||||||||||
Function / homology | Function and homology information ventricular system development / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / [RNA-polymerase]-subunit kinase / RNA Polymerase I Transcription Termination ...ventricular system development / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / [RNA-polymerase]-subunit kinase / RNA Polymerase I Transcription Termination / cyclin-dependent protein serine/threonine kinase regulator activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ATP-dependent activity, acting on DNA / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase II Transcription Elongation / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Formation of RNA Pol II elongation complex / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / male germ cell nucleus / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / positive regulation of smooth muscle cell proliferation / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / Formation of Incision Complex in GG-NER / response to calcium ion / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / G1/S transition of mitotic cell cycle / Cyclin D associated events in G1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription by RNA polymerase II / regulation of cell cycle / protein stabilization / protein kinase activity / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
Authors | Greber BJ / Perez-Bertoldi JM / Lim K / Iavarone AT / Toso DB / Nogales E | |||||||||||||||
Funding support | United States, 4 items
| |||||||||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: The cryoelectron microscopy structure of the human CDK-activating kinase. Authors: Basil J Greber / Juan M Perez-Bertoldi / Kif Lim / Anthony T Iavarone / Daniel B Toso / Eva Nogales / Abstract: The human CDK-activating kinase (CAK), a complex composed of cyclin-dependent kinase (CDK) 7, cyclin H, and MAT1, is a critical regulator of transcription initiation and the cell cycle. It acts by ...The human CDK-activating kinase (CAK), a complex composed of cyclin-dependent kinase (CDK) 7, cyclin H, and MAT1, is a critical regulator of transcription initiation and the cell cycle. It acts by phosphorylating the C-terminal heptapeptide repeat domain of the RNA polymerase II (Pol II) subunit RPB1, which is an important regulatory event in transcription initiation by Pol II, and it phosphorylates the regulatory T-loop of CDKs that control cell cycle progression. Here, we have determined the three-dimensional (3D) structure of the catalytic module of human CAK, revealing the structural basis of its assembly and providing insight into CDK7 activation in this context. The unique third component of the complex, MAT1, substantially extends the interaction interface between CDK7 and cyclin H, explaining its role as a CAK assembly factor, and it forms interactions with the CDK7 T-loop, which may contribute to enhancing CAK activity. We have also determined the structure of the CAK in complex with the covalently bound inhibitor THZ1 in order to provide insight into the binding of inhibitors at the CDK7 active site and to aid in the rational design of therapeutic compounds. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22123.map.gz | 12 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-22123-v30.xml emd-22123.xml | 24.4 KB 24.4 KB | Display Display | EMDB header |
Images | emd_22123.png | 141.7 KB | ||
Masks | emd_22123_msk_1.map | 38.4 MB | Mask map | |
Others | emd_22123_half_map_1.map.gz emd_22123_half_map_2.map.gz | 29.6 MB 29.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22123 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22123 | HTTPS FTP |
-Validation report
Summary document | emd_22123_validation.pdf.gz | 787.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_22123_full_validation.pdf.gz | 786.8 KB | Display | |
Data in XML | emd_22123_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | emd_22123_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22123 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22123 | HTTPS FTP |
-Related structure data
Related structure data | 6xbzMC 6xd3C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10431 (Title: Single-particle cryo-EM of the human CDK-activating kinase in complex with ATP-gamma-S Data size: 3.5 TB Data #1: Unaligned movies of human CAK, dataset 1 [micrographs - multiframe] Data #2: Unaligned movies of human CAK, dataset 2 [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_22123.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Post-processed map, clipped to 150 pixel box size (as used for coordinate refinement) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_22123_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Unfiltered half-map (full size)
File | emd_22123_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unfiltered half-map (full size) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Unfiltered half-map (full size)
File | emd_22123_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unfiltered half-map (full size) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Human CDK-activating kinase
Entire | Name: Human CDK-activating kinase |
---|---|
Components |
|
-Supramolecule #1: Human CDK-activating kinase
Supramolecule | Name: Human CDK-activating kinase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Recombinantly expressed as a trimeric complex in insect cells |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: CDK-activating kinase assembly factor MAT1
Macromolecule | Name: CDK-activating kinase assembly factor MAT1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 38.13234 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDK EVEIRKKVLK IYNKREEDFP SLREYNDFLE EVEEIVFNLT NNVDLDNTKK KMEIYQKENK DVIQKNKLKL T REQEELEE ...String: MGSSHHHHHH ENLYFQSNAM DDQGCPRCKT TKYRNPSLKL MVNVCGHTLC ESCVDLLFVR GAGNCPECGT PLRKSNFRVQ LFEDPTVDK EVEIRKKVLK IYNKREEDFP SLREYNDFLE EVEEIVFNLT NNVDLDNTKK KMEIYQKENK DVIQKNKLKL T REQEELEE ALEVERQENE QRRLFIQKEE QLQQILKRKN KQAFLDELES SDLPVALLLA QHKDRSTQLE MQLEKPKPVK PV TFSTGIK MGQHISLAPI HKLEEALYEY QPLQIETYGP HVPELEMLGR LGYLNHVRAA SPQDLAGGYT SSLACHRALQ DAF SGLFWQ PS |
-Macromolecule #2: Cyclin-H
Macromolecule | Name: Cyclin-H / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.695473 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MYHNSSQKRH WTFSSEEQLA RLRADANRKF RCKAVANGKV LPNDPVFLEP HEEMTLCKYY EKRLLEFCSV FKPAMPRSVV GTACMYFKR FYLNNSVMEY HPRIIMLTCA FLACKVDEFN VSSPQFVGNL RESPLGQEKA LEQILEYELL LIQQLNFHLI V HNPYRPFE ...String: MYHNSSQKRH WTFSSEEQLA RLRADANRKF RCKAVANGKV LPNDPVFLEP HEEMTLCKYY EKRLLEFCSV FKPAMPRSVV GTACMYFKR FYLNNSVMEY HPRIIMLTCA FLACKVDEFN VSSPQFVGNL RESPLGQEKA LEQILEYELL LIQQLNFHLI V HNPYRPFE GFLIDLKTRY PILENPEILR KTADDFLNRI ALTDAYLLYT PSQIALTAIL SSASRAGITM ESYLSESLML KE NRTCLSQ LLDIMKSMRN LVKKYEPPRS EEVAVLKQKL ERCHSAELAL NVITKKRKGY EDDDYVSKKS KHEEEEWTDD DLV ESL |
-Macromolecule #3: Cyclin-dependent kinase 7
Macromolecule | Name: Cyclin-dependent kinase 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 43.731051 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIK LGHRSEAKDG INRTALREIK LLQELSHPNI IGLLDAFGHK SNISLVFDFM ETDLEVIIKD NSLVLTPSHI K AYMLMTLQ ...String: MASWSHPQFE KGGGSGGGSG GGSWSHPQFE KSGGGSENLY FQSNAMALDV KSRAKRYEKL DFLGEGQFAT VYKARDKNTN QIVAIKKIK LGHRSEAKDG INRTALREIK LLQELSHPNI IGLLDAFGHK SNISLVFDFM ETDLEVIIKD NSLVLTPSHI K AYMLMTLQ GLEYLHQHWI LHRDLKPNNL LLDENGVLKL ADFGLAKSFG (SEP)PNRAYTHQV VTRWYRAPEL LFGARMYG V GVDMWAVGCI LAELLLRVPF LPGDSDLDQL TRIFETLGTP TEEQWPDMCS LPDYVTFKSF PGIPLHHIFS AAGDDLLDL IQGLFLFNPC ARITATQALK MKYFSNRPGP TPGCQLPRPN CPVETLKEQS NPALAIKRKR TEALEQGGLP KKLIF |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: AGS |
---|---|
Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.9 Component:
| ||||||||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
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: 3296 / #0 - Average exposure time: 2.0 sec. / #0 - Average electron dose: 69.0 e/Å2 / #0 - Details: 69 frames per movie / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number grids imaged: 1 / #1 - Number real images: 4286 / #1 - Average exposure time: 2.0 sec. / #1 - Average electron dose: 69.0 e/Å2 / #1 - Details: 69 frames per movie |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 72886 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |